Back to Multiple platform build/check report for BioC 3.14 

This page was generated on 20211129 15:05:39 0500 (Mon, 29 Nov 2021).
To the developers/maintainers of the scran package:  Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/scran.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.  Make sure to use the following settings in order to reproduce any error or warning you see on this page. 
Package 1740/2083  Hostname  OS / Arch  INSTALL  BUILD  CHECK  BUILD BIN  
scran 1.22.1 (landing page) Aaron Lun
 nebbiolo2  Linux (Ubuntu 20.04.3 LTS) / x86_64  OK  OK  WARNINGS  
tokay2  Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK  
machv2  macOS 10.14.6 Mojave / x86_64  OK  OK  WARNINGS  OK  
Package: scran 
Version: 1.22.1 
Command: C:\Users\biocbuild\bbs3.14bioc\R\bin\R.exe CMD check forcemultiarch install=check:scran.installout.txt library=C:\Users\biocbuild\bbs3.14bioc\R\library novignettes timings scran_1.22.1.tar.gz 
StartedAt: 20211129 04:44:41 0500 (Mon, 29 Nov 2021) 
EndedAt: 20211129 05:08:57 0500 (Mon, 29 Nov 2021) 
EllapsedTime: 1456.8 seconds 
RetCode: 0 
Status: WARNINGS 
CheckDir: scran.Rcheck 
Warnings: 2 
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs3.14bioc\R\bin\R.exe CMD check forcemultiarch install=check:scran.installout.txt library=C:\Users\biocbuild\bbs3.14bioc\R\library novignettes timings scran_1.22.1.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs3.14bioc/meat/scran.Rcheck' * using R version 4.1.2 (20211101) * using platform: x86_64w64mingw32 (64bit) * using session charset: ISO88591 * using option 'novignettes' * checking for file 'scran/DESCRIPTION' ... OK * this is package 'scran' version '1.22.1' * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking whether package 'scran' can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking 'build' directory ... OK * checking DESCRIPTION metainformation ... OK * checking toplevel files ... OK * checking for leftover files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking R files for nonASCII characters ... OK * checking R files for syntax errors ... OK * loading checks for arch 'i386' ** checking whether the package can be loaded ... OK ** checking whether the package can be loaded with stated dependencies ... OK ** checking whether the package can be unloaded cleanly ... OK ** checking whether the namespace can be loaded with stated dependencies ... OK ** checking whether the namespace can be unloaded cleanly ... OK * loading checks for arch 'x64' ** checking whether the package can be loaded ... OK ** checking whether the package can be loaded with stated dependencies ... OK ** checking whether the package can be unloaded cleanly ... OK ** checking whether the namespace can be loaded with stated dependencies ... OK ** checking whether the namespace can be unloaded cleanly ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd crossreferences ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking line endings in Makefiles ... OK * checking compilation flags in Makevars ... OK * checking for GNU extensions in Makefiles ... OK * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK * checking use of PKG_*FLAGS in Makefiles ... OK * checking compiled code ... NOTE Note: information on .o files for i386 is not available Note: information on .o files for x64 is not available File 'C:/Users/biocbuild/bbs3.14bioc/R/library/scran/libs/i386/scran.dll': Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) Found 'exit', possibly from 'exit' (C), 'stop' (Fortran) Found 'printf', possibly from 'printf' (C) File 'C:/Users/biocbuild/bbs3.14bioc/R/library/scran/libs/x64/scran.dll': Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) Found 'exit', possibly from 'exit' (C), 'stop' (Fortran) Found 'printf', possibly from 'printf' (C) Compiled code should not call entry points which might terminate R nor write to stdout/stderr instead of to the console, nor use Fortran I/O nor system RNGs. The detected symbols are linked into the code but might come from libraries and not actually be called. See 'Writing portable packages' in the 'Writing R Extensions' manual. * checking files in 'vignettes' ... OK * checking examples ... ** running examples for arch 'i386' ... WARNING Found the following significant warnings: Warning: 'combinePValues' is deprecated. Warning: 'combinePValues' is deprecated. Warning: 'combinePValues' is deprecated. Warning: 'combinePValues' is deprecated. Warning: 'correlateNull' is deprecated. Warning: 'correlateNull' is deprecated. Warning: 'correlateNull' is deprecated. Deprecated functions may be defunct as soon as of the next release of R. See ?Deprecated. Examples with CPU (user + system) or elapsed time > 5s user system elapsed cyclone 12.76 1.17 13.94 quickSubCluster 7.03 0.00 7.03 buildSNNGraph 6.67 0.24 6.90 pseudoBulkSpecific 6.59 0.03 6.63 ** running examples for arch 'x64' ... WARNING Found the following significant warnings: Warning: 'combinePValues' is deprecated. Warning: 'combinePValues' is deprecated. Warning: 'combinePValues' is deprecated. Warning: 'combinePValues' is deprecated. Warning: 'correlateNull' is deprecated. Warning: 'correlateNull' is deprecated. Warning: 'correlateNull' is deprecated. Deprecated functions may be defunct as soon as of the next release of R. See ?Deprecated. Examples with CPU (user + system) or elapsed time > 5s user system elapsed cyclone 12.52 0.09 12.61 buildSNNGraph 7.83 0.12 7.95 quickSubCluster 7.12 0.01 7.14 pseudoBulkSpecific 6.82 0.05 6.87 decideTestsPerLabel 5.06 0.05 5.11 * checking for unstated dependencies in 'tests' ... OK * checking tests ... ** running tests for arch 'i386' ... Running 'testthat.R' OK ** running tests for arch 'x64' ... Running 'testthat.R' OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in 'inst/doc' ... OK * checking running R code from vignettes ... SKIPPED * checking rebuilding of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 2 WARNINGs, 1 NOTE See 'C:/Users/biocbuild/bbs3.14bioc/meat/scran.Rcheck/00check.log' for details.
scran.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe O http://155.52.207.166/BBS/3.14/bioc/src/contrib/scran_1.22.1.tar.gz && rm rf scran.buildbinlibdir && mkdir scran.buildbinlibdir && C:\Users\biocbuild\bbs3.14bioc\R\bin\R.exe CMD INSTALL mergemultiarch build library=scran.buildbinlibdir scran_1.22.1.tar.gz && C:\Users\biocbuild\bbs3.14bioc\R\bin\R.exe CMD INSTALL scran_1.22.1.zip && rm scran_1.22.1.tar.gz scran_1.22.1.zip ### ############################################################################## ############################################################################## % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 :: :: :: 0 100 532k 100 532k 0 0 1784k 0 :: :: :: 1792k install for i386 * installing *source* package 'scran' ... ** using staged installation ** libs "C:/rtools40/mingw32/bin/"g++ std=gnu++11 I"C:/Users/BIOCBU~1/BBS3~1.14/R/include" DNDEBUG I'C:/Users/biocbuild/bbs3.14bioc/R/library/Rcpp/include' I'C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include' I'C:/Users/biocbuild/bbs3.14bioc/R/library/BH/include' I'C:/Users/biocbuild/bbs3.14bioc/R/library/dqrng/include' I'C:/Users/biocbuild/bbs3.14bioc/R/library/scuttle/include' I"C:/extsoft/include" O2 Wall mfpmath=sse msse2 mstackrealign c RcppExports.cpp o RcppExports.o "C:/rtools40/mingw32/bin/"g++ std=gnu++11 I"C:/Users/BIOCBU~1/BBS3~1.14/R/include" DNDEBUG I'C:/Users/biocbuild/bbs3.14bioc/R/library/Rcpp/include' I'C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include' I'C:/Users/biocbuild/bbs3.14bioc/R/library/BH/include' I'C:/Users/biocbuild/bbs3.14bioc/R/library/dqrng/include' I'C:/Users/biocbuild/bbs3.14bioc/R/library/scuttle/include' I"C:/extsoft/include" O2 Wall mfpmath=sse msse2 mstackrealign c choose_effect_size.cpp o choose_effect_size.o choose_effect_size.cpp: In instantiation of 'size_t instantiate_list(Rcpp::List, std::vector<T>&, std::__cxx11::string) [with V = Rcpp::Vector<13>; size_t = unsigned int; Rcpp::List = Rcpp::Vector<19>; std::__cxx11::string = std::__cxx11::basic_string<char>]': choose_effect_size.cpp:38:67: required from here choose_effect_size.cpp:13:23: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'unsigned int'} and 'R_xlen_t' {aka 'int'} [Wsigncompare] for (size_t c=0; c<input.size(); ++c) { ~^~~~~~~~~~~~~ choose_effect_size.cpp: In instantiation of 'size_t instantiate_list(Rcpp::List, std::vector<T>&, std::__cxx11::string) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; size_t = unsigned int; Rcpp::List = Rcpp::Vector<19>; std::__cxx11::string = std::__cxx11::basic_string<char>]': choose_effect_size.cpp:67:70: required from here choose_effect_size.cpp:13:23: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'unsigned int'} and 'R_xlen_t' {aka 'int'} [Wsigncompare] "C:/rtools40/mingw32/bin/"g++ std=gnu++11 I"C:/Users/BIOCBU~1/BBS3~1.14/R/include" DNDEBUG I'C:/Users/biocbuild/bbs3.14bioc/R/library/Rcpp/include' I'C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include' I'C:/Users/biocbuild/bbs3.14bioc/R/library/BH/include' I'C:/Users/biocbuild/bbs3.14bioc/R/library/dqrng/include' I'C:/Users/biocbuild/bbs3.14bioc/R/library/scuttle/include' I"C:/extsoft/include" O2 Wall mfpmath=sse msse2 mstackrealign c combine_rho.cpp o combine_rho.o "C:/rtools40/mingw32/bin/"g++ std=gnu++11 I"C:/Users/BIOCBU~1/BBS3~1.14/R/include" DNDEBUG I'C:/Users/biocbuild/bbs3.14bioc/R/library/Rcpp/include' I'C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include' I'C:/Users/biocbuild/bbs3.14bioc/R/library/BH/include' I'C:/Users/biocbuild/bbs3.14bioc/R/library/dqrng/include' I'C:/Users/biocbuild/bbs3.14bioc/R/library/scuttle/include' I"C:/extsoft/include" O2 Wall mfpmath=sse msse2 mstackrealign c compute_blocked_stats.cpp o compute_blocked_stats.o In file included from C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:12, from C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:11, from C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/beachmat.h:24, from compute_blocked_stats.cpp:2: C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of 'beachmat::SparseArraySeed_reader<V, TIT>::SparseArraySeed_reader(Rcpp::RObject) [with V = Rcpp::Vector<13>; TIT = const int*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]': C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:561:56: required from 'beachmat::lin_SparseArraySeed<V, TIT>::lin_SparseArraySeed(Rcpp::RObject) [with V = Rcpp::Vector<13>; TIT = const int*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]' C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:36:39: required from 'std::unique_ptr<_Codecvt> beachmat::read_lin_sparse_block_raw(Rcpp::RObject) [with M = beachmat::lin_matrix; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]' C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:65:63: required from here C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:535:17: warning: comparison of integer expressions of different signedness: 'const size_t' {aka 'const unsigned int'} and 'R_xlen_t' {aka 'int'} [Wsigncompare] if (nnz != x.size()) { C:/Users/biocbuild/bbs3.14bioc/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 unsigned int'} [Wsigncompare] if (lastR <= 0  lastR > NR  lastC <= 0  lastC > NC) { ~~~~~~^~~~ C:/Users/biocbuild/bbs3.14bioc/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 unsigned int'} [Wsigncompare] if (lastR <= 0  lastR > NR  lastC <= 0  lastC > NC) { ~~~~~~^~~~ C:/Users/biocbuild/bbs3.14bioc/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 unsigned int'} [Wsigncompare] for (int v = 0; v < nnz; ++v, ++rowIt, ++colIt, ++xIt) { ~~^~~~~ C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of 'beachmat::SparseArraySeed_reader<V, TIT>::SparseArraySeed_reader(Rcpp::RObject) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]': C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:561:56: required from 'beachmat::lin_SparseArraySeed<V, TIT>::lin_SparseArraySeed(Rcpp::RObject) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]' C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:38:39: required from 'std::unique_ptr<_Codecvt> beachmat::read_lin_sparse_block_raw(Rcpp::RObject) [with M = beachmat::lin_matrix; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]' C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:65:63: required from here C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:535:17: warning: comparison of integer expressions of different signedness: 'const size_t' {aka 'const unsigned int'} and 'R_xlen_t' {aka 'int'} [Wsigncompare] if (nnz != x.size()) { C:/Users/biocbuild/bbs3.14bioc/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 unsigned int'} [Wsigncompare] if (lastR <= 0  lastR > NR  lastC <= 0  lastC > NC) { ~~~~~~^~~~ C:/Users/biocbuild/bbs3.14bioc/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 unsigned int'} [Wsigncompare] if (lastR <= 0  lastR > NR  lastC <= 0  lastC > NC) { ~~~~~~^~~~ C:/Users/biocbuild/bbs3.14bioc/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 unsigned int'} [Wsigncompare] for (int v = 0; v < nnz; ++v, ++rowIt, ++colIt, ++xIt) { ~~^~~~~ C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of 'beachmat::SparseArraySeed_reader<V, TIT>::SparseArraySeed_reader(Rcpp::RObject) [with V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]': C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:561:56: required from 'beachmat::lin_SparseArraySeed<V, TIT>::lin_SparseArraySeed(Rcpp::RObject) [with V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]' C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:40:39: required from 'std::unique_ptr<_Codecvt> beachmat::read_lin_sparse_block_raw(Rcpp::RObject) [with M = beachmat::lin_matrix; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]' C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:65:63: required from here C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:535:17: warning: comparison of integer expressions of different signedness: 'const size_t' {aka 'const unsigned int'} and 'R_xlen_t' {aka 'int'} [Wsigncompare] if (nnz != x.size()) { C:/Users/biocbuild/bbs3.14bioc/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 unsigned int'} [Wsigncompare] if (lastR <= 0  lastR > NR  lastC <= 0  lastC > NC) { ~~~~~~^~~~ C:/Users/biocbuild/bbs3.14bioc/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 unsigned int'} [Wsigncompare] if (lastR <= 0  lastR > NR  lastC <= 0  lastC > NC) { ~~~~~~^~~~ C:/Users/biocbuild/bbs3.14bioc/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 unsigned int'} [Wsigncompare] for (int v = 0; v < nnz; ++v, ++rowIt, ++colIt, ++xIt) { ~~^~~~~ C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of 'beachmat::sparse_index<OUT, I> beachmat::Csparse_core<TIT, I, P>::get_row(size_t, ALT, I*, size_t, size_t) [with OUT = const int*; ALT = int*; TIT = const double*; I = int; P = unsigned int; size_t = unsigned int]': C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:650:73: required from 'beachmat::sparse_index<OUT, int> beachmat::SparseArraySeed_reader<V, TIT>::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 = unsigned int]' C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:596:82: required from 'beachmat::sparse_index<const int*, int> beachmat::lin_SparseArraySeed<V, TIT>::get_row(size_t, int*, int*, size_t, size_t) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; size_t = unsigned int]' C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:595:35: required from here C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison of integer expressions of different signedness: 'const int' and 'const unsigned int' [Wsigncompare] if (idex != *pIt && static_cast<size_t>(i[idex]) == r) { ~~~~~^~~~~~~ C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of 'beachmat::sparse_index<OUT, I> beachmat::Csparse_core<TIT, I, P>::get_row(size_t, ALT, I*, size_t, size_t) [with OUT = const double*; ALT = double*; TIT = const double*; I = int; P = unsigned int; size_t = unsigned int]': C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:650:73: required from 'beachmat::sparse_index<OUT, int> beachmat::SparseArraySeed_reader<V, TIT>::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 = unsigned int]' C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:602:85: required from 'beachmat::sparse_index<const double*, int> beachmat::lin_SparseArraySeed<V, TIT>::get_row(size_t, double*, int*, size_t, size_t) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; size_t = unsigned int]' C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:601:38: required from here C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison of integer expressions of different signedness: 'const int' and 'const unsigned int' [Wsigncompare] C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of 'beachmat::sparse_index<OUT, I> beachmat::Csparse_core<TIT, I, P>::get_row(size_t, ALT, I*, size_t, size_t) [with OUT = const int*; ALT = int*; TIT = const int*; I = int; P = unsigned int; size_t = unsigned int]': C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:650:73: required from 'beachmat::sparse_index<OUT, int> beachmat::SparseArraySeed_reader<V, TIT>::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 = unsigned int]' C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:596:82: required from 'beachmat::sparse_index<const int*, int> beachmat::lin_SparseArraySeed<V, TIT>::get_row(size_t, int*, int*, size_t, size_t) [with V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; size_t = unsigned int]' C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:595:35: required from here C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison of integer expressions of different signedness: 'const int' and 'const unsigned int' [Wsigncompare] C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of 'beachmat::sparse_index<OUT, I> beachmat::Csparse_core<TIT, I, P>::get_row(size_t, ALT, I*, size_t, size_t) [with OUT = const double*; ALT = double*; TIT = const int*; I = int; P = unsigned int; size_t = unsigned int]': C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:650:73: required from 'beachmat::sparse_index<OUT, int> beachmat::SparseArraySeed_reader<V, TIT>::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 = unsigned int]' C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:602:85: required from 'beachmat::sparse_index<const double*, int> beachmat::lin_SparseArraySeed<V, TIT>::get_row(size_t, double*, int*, size_t, size_t) [with V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; size_t = unsigned int]' C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:601:38: required from here C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison of integer expressions of different signedness: 'const int' and 'const unsigned int' [Wsigncompare] "C:/rtools40/mingw32/bin/"g++ std=gnu++11 I"C:/Users/BIOCBU~1/BBS3~1.14/R/include" DNDEBUG I'C:/Users/biocbuild/bbs3.14bioc/R/library/Rcpp/include' I'C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include' I'C:/Users/biocbuild/bbs3.14bioc/R/library/BH/include' I'C:/Users/biocbuild/bbs3.14bioc/R/library/dqrng/include' I'C:/Users/biocbuild/bbs3.14bioc/R/library/scuttle/include' I"C:/extsoft/include" O2 Wall mfpmath=sse msse2 mstackrealign c compute_residual_stats.cpp o compute_residual_stats.o In file included from C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:12, from C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:11, from C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/beachmat.h:24, from compute_residual_stats.cpp:2: C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of 'beachmat::SparseArraySeed_reader<V, TIT>::SparseArraySeed_reader(Rcpp::RObject) [with V = Rcpp::Vector<13>; TIT = const int*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]': C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:561:56: required from 'beachmat::lin_SparseArraySeed<V, TIT>::lin_SparseArraySeed(Rcpp::RObject) [with V = Rcpp::Vector<13>; TIT = const int*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]' C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:36:39: required from 'std::unique_ptr<_Codecvt> beachmat::read_lin_sparse_block_raw(Rcpp::RObject) [with M = beachmat::lin_matrix; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]' C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:65:63: required from here C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:535:17: warning: comparison of integer expressions of different signedness: 'const size_t' {aka 'const unsigned int'} and 'R_xlen_t' {aka 'int'} [Wsigncompare] if (nnz != x.size()) { C:/Users/biocbuild/bbs3.14bioc/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 unsigned int'} [Wsigncompare] if (lastR <= 0  lastR > NR  lastC <= 0  lastC > NC) { ~~~~~~^~~~ C:/Users/biocbuild/bbs3.14bioc/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 unsigned int'} [Wsigncompare] if (lastR <= 0  lastR > NR  lastC <= 0  lastC > NC) { ~~~~~~^~~~ C:/Users/biocbuild/bbs3.14bioc/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 unsigned int'} [Wsigncompare] for (int v = 0; v < nnz; ++v, ++rowIt, ++colIt, ++xIt) { ~~^~~~~ C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of 'beachmat::SparseArraySeed_reader<V, TIT>::SparseArraySeed_reader(Rcpp::RObject) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]': C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:561:56: required from 'beachmat::lin_SparseArraySeed<V, TIT>::lin_SparseArraySeed(Rcpp::RObject) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]' C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:38:39: required from 'std::unique_ptr<_Codecvt> beachmat::read_lin_sparse_block_raw(Rcpp::RObject) [with M = beachmat::lin_matrix; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]' C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:65:63: required from here C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:535:17: warning: comparison of integer expressions of different signedness: 'const size_t' {aka 'const unsigned int'} and 'R_xlen_t' {aka 'int'} [Wsigncompare] if (nnz != x.size()) { C:/Users/biocbuild/bbs3.14bioc/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 unsigned int'} [Wsigncompare] if (lastR <= 0  lastR > NR  lastC <= 0  lastC > NC) { ~~~~~~^~~~ C:/Users/biocbuild/bbs3.14bioc/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 unsigned int'} [Wsigncompare] if (lastR <= 0  lastR > NR  lastC <= 0  lastC > NC) { ~~~~~~^~~~ C:/Users/biocbuild/bbs3.14bioc/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 unsigned int'} [Wsigncompare] for (int v = 0; v < nnz; ++v, ++rowIt, ++colIt, ++xIt) { ~~^~~~~ C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of 'beachmat::SparseArraySeed_reader<V, TIT>::SparseArraySeed_reader(Rcpp::RObject) [with V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]': C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:561:56: required from 'beachmat::lin_SparseArraySeed<V, TIT>::lin_SparseArraySeed(Rcpp::RObject) [with V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]' C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:40:39: required from 'std::unique_ptr<_Codecvt> beachmat::read_lin_sparse_block_raw(Rcpp::RObject) [with M = beachmat::lin_matrix; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]' C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:65:63: required from here C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:535:17: warning: comparison of integer expressions of different signedness: 'const size_t' {aka 'const unsigned int'} and 'R_xlen_t' {aka 'int'} [Wsigncompare] if (nnz != x.size()) { C:/Users/biocbuild/bbs3.14bioc/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 unsigned int'} [Wsigncompare] if (lastR <= 0  lastR > NR  lastC <= 0  lastC > NC) { ~~~~~~^~~~ C:/Users/biocbuild/bbs3.14bioc/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 unsigned int'} [Wsigncompare] if (lastR <= 0  lastR > NR  lastC <= 0  lastC > NC) { ~~~~~~^~~~ C:/Users/biocbuild/bbs3.14bioc/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 unsigned int'} [Wsigncompare] for (int v = 0; v < nnz; ++v, ++rowIt, ++colIt, ++xIt) { ~~^~~~~ C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of 'beachmat::sparse_index<OUT, I> beachmat::Csparse_core<TIT, I, P>::get_row(size_t, ALT, I*, size_t, size_t) [with OUT = const int*; ALT = int*; TIT = const double*; I = int; P = unsigned int; size_t = unsigned int]': C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:650:73: required from 'beachmat::sparse_index<OUT, int> beachmat::SparseArraySeed_reader<V, TIT>::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 = unsigned int]' C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:596:82: required from 'beachmat::sparse_index<const int*, int> beachmat::lin_SparseArraySeed<V, TIT>::get_row(size_t, int*, int*, size_t, size_t) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; size_t = unsigned int]' C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:595:35: required from here C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison of integer expressions of different signedness: 'const int' and 'const unsigned int' [Wsigncompare] if (idex != *pIt && static_cast<size_t>(i[idex]) == r) { ~~~~~^~~~~~~ C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of 'beachmat::sparse_index<OUT, I> beachmat::Csparse_core<TIT, I, P>::get_row(size_t, ALT, I*, size_t, size_t) [with OUT = const double*; ALT = double*; TIT = const double*; I = int; P = unsigned int; size_t = unsigned int]': C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:650:73: required from 'beachmat::sparse_index<OUT, int> beachmat::SparseArraySeed_reader<V, TIT>::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 = unsigned int]' C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:602:85: required from 'beachmat::sparse_index<const double*, int> beachmat::lin_SparseArraySeed<V, TIT>::get_row(size_t, double*, int*, size_t, size_t) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; size_t = unsigned int]' C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:601:38: required from here C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison of integer expressions of different signedness: 'const int' and 'const unsigned int' [Wsigncompare] C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of 'beachmat::sparse_index<OUT, I> beachmat::Csparse_core<TIT, I, P>::get_row(size_t, ALT, I*, size_t, size_t) [with OUT = const int*; ALT = int*; TIT = const int*; I = int; P = unsigned int; size_t = unsigned int]': C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:650:73: required from 'beachmat::sparse_index<OUT, int> beachmat::SparseArraySeed_reader<V, TIT>::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 = unsigned int]' C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:596:82: required from 'beachmat::sparse_index<const int*, int> beachmat::lin_SparseArraySeed<V, TIT>::get_row(size_t, int*, int*, size_t, size_t) [with V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; size_t = unsigned int]' C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:595:35: required from here C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison of integer expressions of different signedness: 'const int' and 'const unsigned int' [Wsigncompare] C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of 'beachmat::sparse_index<OUT, I> beachmat::Csparse_core<TIT, I, P>::get_row(size_t, ALT, I*, size_t, size_t) [with OUT = const double*; ALT = double*; TIT = const int*; I = int; P = unsigned int; size_t = unsigned int]': C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:650:73: required from 'beachmat::sparse_index<OUT, int> beachmat::SparseArraySeed_reader<V, TIT>::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 = unsigned int]' C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:602:85: required from 'beachmat::sparse_index<const double*, int> beachmat::lin_SparseArraySeed<V, TIT>::get_row(size_t, double*, int*, size_t, size_t) [with V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; size_t = unsigned int]' C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:601:38: required from here C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison of integer expressions of different signedness: 'const int' and 'const unsigned int' [Wsigncompare] "C:/rtools40/mingw32/bin/"g++ std=gnu++11 I"C:/Users/BIOCBU~1/BBS3~1.14/R/include" DNDEBUG I'C:/Users/biocbuild/bbs3.14bioc/R/library/Rcpp/include' I'C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include' I'C:/Users/biocbuild/bbs3.14bioc/R/library/BH/include' I'C:/Users/biocbuild/bbs3.14bioc/R/library/dqrng/include' I'C:/Users/biocbuild/bbs3.14bioc/R/library/scuttle/include' I"C:/extsoft/include" O2 Wall mfpmath=sse msse2 mstackrealign c compute_rho_null.cpp o compute_rho_null.o In file included from C:/Users/biocbuild/bbs3.14bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23, from C:/Users/biocbuild/bbs3.14bioc/R/library/BH/include/boost/mpl/arg.hpp:25, from C:/Users/biocbuild/bbs3.14bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24, from C:/Users/biocbuild/bbs3.14bioc/R/library/BH/include/boost/mpl/apply.hpp:24, from C:/Users/biocbuild/bbs3.14bioc/R/library/BH/include/boost/mpl/aux_/iter_apply.hpp:17, from C:/Users/biocbuild/bbs3.14bioc/R/library/BH/include/boost/mpl/aux_/find_if_pred.hpp:14, from C:/Users/biocbuild/bbs3.14bioc/R/library/BH/include/boost/mpl/find_if.hpp:17, from C:/Users/biocbuild/bbs3.14bioc/R/library/BH/include/boost/mpl/find.hpp:17, from C:/Users/biocbuild/bbs3.14bioc/R/library/BH/include/boost/mpl/aux_/contains_impl.hpp:20, from C:/Users/biocbuild/bbs3.14bioc/R/library/BH/include/boost/mpl/contains.hpp:20, from C:/Users/biocbuild/bbs3.14bioc/R/library/BH/include/boost/math/policies/policy.hpp:10, from C:/Users/biocbuild/bbs3.14bioc/R/library/BH/include/boost/math/special_functions/math_fwd.hpp:29, from C:/Users/biocbuild/bbs3.14bioc/R/library/BH/include/boost/math/special_functions/fpclassify.hpp:19, from C:/Users/biocbuild/bbs3.14bioc/R/library/BH/include/boost/random/hyperexponential_distribution.hpp:22, from C:/Users/biocbuild/bbs3.14bioc/R/library/BH/include/boost/random.hpp:69, from rand_custom.h:6, from compute_rho_null.cpp:3: C:/Users/biocbuild/bbs3.14bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [Wparentheses] failed ************ (Pred::************ ^ C:/Users/biocbuild/bbs3.14bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [Wparentheses] failed ************ (boost::mpl::not_<Pred>::************ ^ "C:/rtools40/mingw32/bin/"g++ std=gnu++11 I"C:/Users/BIOCBU~1/BBS3~1.14/R/include" DNDEBUG I'C:/Users/biocbuild/bbs3.14bioc/R/library/Rcpp/include' I'C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include' I'C:/Users/biocbuild/bbs3.14bioc/R/library/BH/include' I'C:/Users/biocbuild/bbs3.14bioc/R/library/dqrng/include' I'C:/Users/biocbuild/bbs3.14bioc/R/library/scuttle/include' I"C:/extsoft/include" O2 Wall mfpmath=sse msse2 mstackrealign c cyclone_scores.cpp o cyclone_scores.o In file included from C:/Users/biocbuild/bbs3.14bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23, from C:/Users/biocbuild/bbs3.14bioc/R/library/BH/include/boost/mpl/arg.hpp:25, from C:/Users/biocbuild/bbs3.14bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24, from C:/Users/biocbuild/bbs3.14bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16, from C:/Users/biocbuild/bbs3.14bioc/R/library/BH/include/boost/iterator/iterator_concepts.hpp:10, from C:/Users/biocbuild/bbs3.14bioc/R/library/BH/include/boost/range/concepts.hpp:20, from C:/Users/biocbuild/bbs3.14bioc/R/library/BH/include/boost/range/algorithm.hpp:29, from cyclone_scores.cpp:4: C:/Users/biocbuild/bbs3.14bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [Wparentheses] failed ************ (Pred::************ ^ C:/Users/biocbuild/bbs3.14bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [Wparentheses] failed ************ (boost::mpl::not_<Pred>::************ ^ In file included from C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:12, from C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:11, from C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/beachmat.h:24, from cyclone_scores.cpp:3: C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of 'beachmat::SparseArraySeed_reader<V, TIT>::SparseArraySeed_reader(Rcpp::RObject) [with V = Rcpp::Vector<13>; TIT = const int*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]': C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:561:56: required from 'beachmat::lin_SparseArraySeed<V, TIT>::lin_SparseArraySeed(Rcpp::RObject) [with V = Rcpp::Vector<13>; TIT = const int*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]' C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:36:39: required from 'std::unique_ptr<_Codecvt> beachmat::read_lin_sparse_block_raw(Rcpp::RObject) [with M = beachmat::lin_matrix; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]' C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:65:63: required from here C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:535:17: warning: comparison of integer expressions of different signedness: 'const size_t' {aka 'const unsigned int'} and 'R_xlen_t' {aka 'int'} [Wsigncompare] if (nnz != x.size()) { C:/Users/biocbuild/bbs3.14bioc/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 unsigned int'} [Wsigncompare] if (lastR <= 0  lastR > NR  lastC <= 0  lastC > NC) { ~~~~~~^~~~ C:/Users/biocbuild/bbs3.14bioc/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 unsigned int'} [Wsigncompare] if (lastR <= 0  lastR > NR  lastC <= 0  lastC > NC) { ~~~~~~^~~~ C:/Users/biocbuild/bbs3.14bioc/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 unsigned int'} [Wsigncompare] for (int v = 0; v < nnz; ++v, ++rowIt, ++colIt, ++xIt) { ~~^~~~~ C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of 'beachmat::SparseArraySeed_reader<V, TIT>::SparseArraySeed_reader(Rcpp::RObject) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]': C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:561:56: required from 'beachmat::lin_SparseArraySeed<V, TIT>::lin_SparseArraySeed(Rcpp::RObject) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]' C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:38:39: required from 'std::unique_ptr<_Codecvt> beachmat::read_lin_sparse_block_raw(Rcpp::RObject) [with M = beachmat::lin_matrix; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]' C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:65:63: required from here C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:535:17: warning: comparison of integer expressions of different signedness: 'const size_t' {aka 'const unsigned int'} and 'R_xlen_t' {aka 'int'} [Wsigncompare] if (nnz != x.size()) { C:/Users/biocbuild/bbs3.14bioc/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 unsigned int'} [Wsigncompare] if (lastR <= 0  lastR > NR  lastC <= 0  lastC > NC) { ~~~~~~^~~~ C:/Users/biocbuild/bbs3.14bioc/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 unsigned int'} [Wsigncompare] if (lastR <= 0  lastR > NR  lastC <= 0  lastC > NC) { ~~~~~~^~~~ C:/Users/biocbuild/bbs3.14bioc/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 unsigned int'} [Wsigncompare] for (int v = 0; v < nnz; ++v, ++rowIt, ++colIt, ++xIt) { ~~^~~~~ C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of 'beachmat::SparseArraySeed_reader<V, TIT>::SparseArraySeed_reader(Rcpp::RObject) [with V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]': C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:561:56: required from 'beachmat::lin_SparseArraySeed<V, TIT>::lin_SparseArraySeed(Rcpp::RObject) [with V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]' C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:40:39: required from 'std::unique_ptr<_Codecvt> beachmat::read_lin_sparse_block_raw(Rcpp::RObject) [with M = beachmat::lin_matrix; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]' C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:65:63: required from here C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:535:17: warning: comparison of integer expressions of different signedness: 'const size_t' {aka 'const unsigned int'} and 'R_xlen_t' {aka 'int'} [Wsigncompare] if (nnz != x.size()) { C:/Users/biocbuild/bbs3.14bioc/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 unsigned int'} [Wsigncompare] if (lastR <= 0  lastR > NR  lastC <= 0  lastC > NC) { ~~~~~~^~~~ C:/Users/biocbuild/bbs3.14bioc/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 unsigned int'} [Wsigncompare] if (lastR <= 0  lastR > NR  lastC <= 0  lastC > NC) { ~~~~~~^~~~ C:/Users/biocbuild/bbs3.14bioc/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 unsigned int'} [Wsigncompare] for (int v = 0; v < nnz; ++v, ++rowIt, ++colIt, ++xIt) { ~~^~~~~ C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of 'beachmat::sparse_index<OUT, I> beachmat::Csparse_core<TIT, I, P>::get_row(size_t, ALT, I*, size_t, size_t) [with OUT = const int*; ALT = int*; TIT = const double*; I = int; P = unsigned int; size_t = unsigned int]': C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:650:73: required from 'beachmat::sparse_index<OUT, int> beachmat::SparseArraySeed_reader<V, TIT>::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 = unsigned int]' C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:596:82: required from 'beachmat::sparse_index<const int*, int> beachmat::lin_SparseArraySeed<V, TIT>::get_row(size_t, int*, int*, size_t, size_t) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; size_t = unsigned int]' C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:595:35: required from here C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison of integer expressions of different signedness: 'const int' and 'const unsigned int' [Wsigncompare] if (idex != *pIt && static_cast<size_t>(i[idex]) == r) { ~~~~~^~~~~~~ C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of 'beachmat::sparse_index<OUT, I> beachmat::Csparse_core<TIT, I, P>::get_row(size_t, ALT, I*, size_t, size_t) [with OUT = const double*; ALT = double*; TIT = const double*; I = int; P = unsigned int; size_t = unsigned int]': C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:650:73: required from 'beachmat::sparse_index<OUT, int> beachmat::SparseArraySeed_reader<V, TIT>::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 = unsigned int]' C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:602:85: required from 'beachmat::sparse_index<const double*, int> beachmat::lin_SparseArraySeed<V, TIT>::get_row(size_t, double*, int*, size_t, size_t) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; size_t = unsigned int]' C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:601:38: required from here C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison of integer expressions of different signedness: 'const int' and 'const unsigned int' [Wsigncompare] C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of 'beachmat::sparse_index<OUT, I> beachmat::Csparse_core<TIT, I, P>::get_row(size_t, ALT, I*, size_t, size_t) [with OUT = const int*; ALT = int*; TIT = const int*; I = int; P = unsigned int; size_t = unsigned int]': C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:650:73: required from 'beachmat::sparse_index<OUT, int> beachmat::SparseArraySeed_reader<V, TIT>::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 = unsigned int]' C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:596:82: required from 'beachmat::sparse_index<const int*, int> beachmat::lin_SparseArraySeed<V, TIT>::get_row(size_t, int*, int*, size_t, size_t) [with V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; size_t = unsigned int]' C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:595:35: required from here C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison of integer expressions of different signedness: 'const int' and 'const unsigned int' [Wsigncompare] C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of 'beachmat::sparse_index<OUT, I> beachmat::Csparse_core<TIT, I, P>::get_row(size_t, ALT, I*, size_t, size_t) [with OUT = const double*; ALT = double*; TIT = const int*; I = int; P = unsigned int; size_t = unsigned int]': C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:650:73: required from 'beachmat::sparse_index<OUT, int> beachmat::SparseArraySeed_reader<V, TIT>::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 = unsigned int]' C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:602:85: required from 'beachmat::sparse_index<const double*, int> beachmat::lin_SparseArraySeed<V, TIT>::get_row(size_t, double*, int*, size_t, size_t) [with V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; size_t = unsigned int]' C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:601:38: required from here C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison of integer expressions of different signedness: 'const int' and 'const unsigned int' [Wsigncompare] "C:/rtools40/mingw32/bin/"g++ std=gnu++11 I"C:/Users/BIOCBU~1/BBS3~1.14/R/include" DNDEBUG I'C:/Users/biocbuild/bbs3.14bioc/R/library/Rcpp/include' I'C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include' I'C:/Users/biocbuild/bbs3.14bioc/R/library/BH/include' I'C:/Users/biocbuild/bbs3.14bioc/R/library/dqrng/include' I'C:/Users/biocbuild/bbs3.14bioc/R/library/scuttle/include' I"C:/extsoft/include" O2 Wall mfpmath=sse msse2 mstackrealign c overlap_exprs.cpp o overlap_exprs.o overlap_exprs.cpp: In function 'Rcpp::NumericMatrix overlap_exprs_paired(Rcpp::RObject, Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::List, double)': overlap_exprs.cpp:214:27: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'unsigned int'} and 'R_xlen_t' {aka 'int'} [Wsigncompare] for (size_t i=0; i<left.size(); ++i, ++oIt) { ~^~~~~~~~~~~~ overlap_exprs.cpp:202:18: warning: unused variable 'ngroups' [Wunusedvariable] const size_t ngroups=groups.size(); ^~~~~~~ In file included from C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:12, from C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:11, from C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/beachmat.h:24, from overlap_exprs.cpp:3: C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of 'beachmat::SparseArraySeed_reader<V, TIT>::SparseArraySeed_reader(Rcpp::RObject) [with V = Rcpp::Vector<13>; TIT = const int*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]': C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:561:56: required from 'beachmat::lin_SparseArraySeed<V, TIT>::lin_SparseArraySeed(Rcpp::RObject) [with V = Rcpp::Vector<13>; TIT = const int*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]' C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:36:39: required from 'std::unique_ptr<_Codecvt> beachmat::read_lin_sparse_block_raw(Rcpp::RObject) [with M = beachmat::lin_matrix; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]' C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:65:63: required from here C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:535:17: warning: comparison of integer expressions of different signedness: 'const size_t' {aka 'const unsigned int'} and 'R_xlen_t' {aka 'int'} [Wsigncompare] if (nnz != x.size()) { C:/Users/biocbuild/bbs3.14bioc/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 unsigned int'} [Wsigncompare] if (lastR <= 0  lastR > NR  lastC <= 0  lastC > NC) { ~~~~~~^~~~ C:/Users/biocbuild/bbs3.14bioc/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 unsigned int'} [Wsigncompare] if (lastR <= 0  lastR > NR  lastC <= 0  lastC > NC) { ~~~~~~^~~~ C:/Users/biocbuild/bbs3.14bioc/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 unsigned int'} [Wsigncompare] for (int v = 0; v < nnz; ++v, ++rowIt, ++colIt, ++xIt) { ~~^~~~~ C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of 'beachmat::SparseArraySeed_reader<V, TIT>::SparseArraySeed_reader(Rcpp::RObject) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]': C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:561:56: required from 'beachmat::lin_SparseArraySeed<V, TIT>::lin_SparseArraySeed(Rcpp::RObject) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]' C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:38:39: required from 'std::unique_ptr<_Codecvt> beachmat::read_lin_sparse_block_raw(Rcpp::RObject) [with M = beachmat::lin_matrix; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]' C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:65:63: required from here C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:535:17: warning: comparison of integer expressions of different signedness: 'const size_t' {aka 'const unsigned int'} and 'R_xlen_t' {aka 'int'} [Wsigncompare] if (nnz != x.size()) { C:/Users/biocbuild/bbs3.14bioc/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 unsigned int'} [Wsigncompare] if (lastR <= 0  lastR > NR  lastC <= 0  lastC > NC) { ~~~~~~^~~~ C:/Users/biocbuild/bbs3.14bioc/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 unsigned int'} [Wsigncompare] if (lastR <= 0  lastR > NR  lastC <= 0  lastC > NC) { ~~~~~~^~~~ C:/Users/biocbuild/bbs3.14bioc/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 unsigned int'} [Wsigncompare] for (int v = 0; v < nnz; ++v, ++rowIt, ++colIt, ++xIt) { ~~^~~~~ C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of 'beachmat::SparseArraySeed_reader<V, TIT>::SparseArraySeed_reader(Rcpp::RObject) [with V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]': C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:561:56: required from 'beachmat::lin_SparseArraySeed<V, TIT>::lin_SparseArraySeed(Rcpp::RObject) [with V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]' C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:40:39: required from 'std::unique_ptr<_Codecvt> beachmat::read_lin_sparse_block_raw(Rcpp::RObject) [with M = beachmat::lin_matrix; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]' C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:65:63: required from here C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:535:17: warning: comparison of integer expressions of different signedness: 'const size_t' {aka 'const unsigned int'} and 'R_xlen_t' {aka 'int'} [Wsigncompare] if (nnz != x.size()) { C:/Users/biocbuild/bbs3.14bioc/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 unsigned int'} [Wsigncompare] if (lastR <= 0  lastR > NR  lastC <= 0  lastC > NC) { ~~~~~~^~~~ C:/Users/biocbuild/bbs3.14bioc/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 unsigned int'} [Wsigncompare] if (lastR <= 0  lastR > NR  lastC <= 0  lastC > NC) { ~~~~~~^~~~ C:/Users/biocbuild/bbs3.14bioc/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 unsigned int'} [Wsigncompare] for (int v = 0; v < nnz; ++v, ++rowIt, ++colIt, ++xIt) { ~~^~~~~ C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of 'beachmat::sparse_index<OUT, I> beachmat::Csparse_core<TIT, I, P>::get_row(size_t, ALT, I*, size_t, size_t) [with OUT = const int*; ALT = int*; TIT = const double*; I = int; P = unsigned int; size_t = unsigned int]': C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:650:73: required from 'beachmat::sparse_index<OUT, int> beachmat::SparseArraySeed_reader<V, TIT>::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 = unsigned int]' C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:596:82: required from 'beachmat::sparse_index<const int*, int> beachmat::lin_SparseArraySeed<V, TIT>::get_row(size_t, int*, int*, size_t, size_t) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; size_t = unsigned int]' C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:595:35: required from here C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison of integer expressions of different signedness: 'const int' and 'const unsigned int' [Wsigncompare] if (idex != *pIt && static_cast<size_t>(i[idex]) == r) { ~~~~~^~~~~~~ C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of 'beachmat::sparse_index<OUT, I> beachmat::Csparse_core<TIT, I, P>::get_row(size_t, ALT, I*, size_t, size_t) [with OUT = const double*; ALT = double*; TIT = const double*; I = int; P = unsigned int; size_t = unsigned int]': C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:650:73: required from 'beachmat::sparse_index<OUT, int> beachmat::SparseArraySeed_reader<V, TIT>::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 = unsigned int]' C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:602:85: required from 'beachmat::sparse_index<const double*, int> beachmat::lin_SparseArraySeed<V, TIT>::get_row(size_t, double*, int*, size_t, size_t) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; size_t = unsigned int]' C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:601:38: required from here C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison of integer expressions of different signedness: 'const int' and 'const unsigned int' [Wsigncompare] C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of 'beachmat::sparse_index<OUT, I> beachmat::Csparse_core<TIT, I, P>::get_row(size_t, ALT, I*, size_t, size_t) [with OUT = const int*; ALT = int*; TIT = const int*; I = int; P = unsigned int; size_t = unsigned int]': C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:650:73: required from 'beachmat::sparse_index<OUT, int> beachmat::SparseArraySeed_reader<V, TIT>::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 = unsigned int]' C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:596:82: required from 'beachmat::sparse_index<const int*, int> beachmat::lin_SparseArraySeed<V, TIT>::get_row(size_t, int*, int*, size_t, size_t) [with V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; size_t = unsigned int]' C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:595:35: required from here C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison of integer expressions of different signedness: 'const int' and 'const unsigned int' [Wsigncompare] C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of 'beachmat::sparse_index<OUT, I> beachmat::Csparse_core<TIT, I, P>::get_row(size_t, ALT, I*, size_t, size_t) [with OUT = const double*; ALT = double*; TIT = const int*; I = int; P = unsigned int; size_t = unsigned int]': C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:650:73: required from 'beachmat::sparse_index<OUT, int> beachmat::SparseArraySeed_reader<V, TIT>::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 = unsigned int]' C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:602:85: required from 'beachmat::sparse_index<const double*, int> beachmat::lin_SparseArraySeed<V, TIT>::get_row(size_t, double*, int*, size_t, size_t) [with V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; size_t = unsigned int]' C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:601:38: required from here C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison of integer expressions of different signedness: 'const int' and 'const unsigned int' [Wsigncompare] "C:/rtools40/mingw32/bin/"g++ std=gnu++11 I"C:/Users/BIOCBU~1/BBS3~1.14/R/include" DNDEBUG I'C:/Users/biocbuild/bbs3.14bioc/R/library/Rcpp/include' I'C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include' I'C:/Users/biocbuild/bbs3.14bioc/R/library/BH/include' I'C:/Users/biocbuild/bbs3.14bioc/R/library/dqrng/include' I'C:/Users/biocbuild/bbs3.14bioc/R/library/scuttle/include' I"C:/extsoft/include" O2 Wall mfpmath=sse msse2 mstackrealign c rand_custom.cpp o rand_custom.o In file included from C:/Users/biocbuild/bbs3.14bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23, from C:/Users/biocbuild/bbs3.14bioc/R/library/BH/include/boost/mpl/arg.hpp:25, from C:/Users/biocbuild/bbs3.14bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24, from C:/Users/biocbuild/bbs3.14bioc/R/library/BH/include/boost/mpl/apply.hpp:24, from C:/Users/biocbuild/bbs3.14bioc/R/library/BH/include/boost/mpl/aux_/iter_apply.hpp:17, from C:/Users/biocbuild/bbs3.14bioc/R/library/BH/include/boost/mpl/aux_/find_if_pred.hpp:14, from C:/Users/biocbuild/bbs3.14bioc/R/library/BH/include/boost/mpl/find_if.hpp:17, from C:/Users/biocbuild/bbs3.14bioc/R/library/BH/include/boost/mpl/find.hpp:17, from C:/Users/biocbuild/bbs3.14bioc/R/library/BH/include/boost/mpl/aux_/contains_impl.hpp:20, from C:/Users/biocbuild/bbs3.14bioc/R/library/BH/include/boost/mpl/contains.hpp:20, from C:/Users/biocbuild/bbs3.14bioc/R/library/BH/include/boost/math/policies/policy.hpp:10, from C:/Users/biocbuild/bbs3.14bioc/R/library/BH/include/boost/math/special_functions/math_fwd.hpp:29, from C:/Users/biocbuild/bbs3.14bioc/R/library/BH/include/boost/math/special_functions/fpclassify.hpp:19, from C:/Users/biocbuild/bbs3.14bioc/R/library/BH/include/boost/random/hyperexponential_distribution.hpp:22, from C:/Users/biocbuild/bbs3.14bioc/R/library/BH/include/boost/random.hpp:69, from rand_custom.h:6, from rand_custom.cpp:1: C:/Users/biocbuild/bbs3.14bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [Wparentheses] failed ************ (Pred::************ ^ C:/Users/biocbuild/bbs3.14bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [Wparentheses] failed ************ (boost::mpl::not_<Pred>::************ ^ C:/rtools40/mingw32/bin/g++ shared s staticlibgcc o scran.dll tmp.def RcppExports.o choose_effect_size.o combine_rho.o compute_blocked_stats.o compute_residual_stats.o compute_rho_null.o cyclone_scores.o overlap_exprs.o rand_custom.o LC:/Users/BIOCBU~1/BBS3~1.14/R/bin/i386 lRlapack LC:/Users/BIOCBU~1/BBS3~1.14/R/bin/i386 lRblas lgfortran lm lquadmath LC:/extsoft/lib/i386 LC:/extsoft/lib LC:/Users/BIOCBU~1/BBS3~1.14/R/bin/i386 lR installing to C:/Users/biocbuild/bbs3.14bioc/meat/scran.buildbinlibdir/00LOCKscran/00new/scran/libs/i386 ** R ** inst ** bytecompile and prepare package for lazy loading ** help *** installing help indices converting help for package 'scran' finding HTML links ... done DM html buildSNNGraph html finding level2 HTML links ... done clusterCells html combineBlocks html combineMarkers html combinePValues html combineVar html computeMinRank html computeSumFactors html convertTo html correlateGenes html correlateNull html correlatePairs html cyclone html decideTestsPerLabel html defunct html denoisePCA html findMarkers html fitTrendCV2 html fitTrendPoisson html fitTrendVar html fixedPCA html gene_selection html getClusteredPCs html getMarkerEffects html getTopHVGs html getTopMarkers html logBH html modelGeneCV2 html modelGeneCV2WithSpikes html modelGeneVar html modelGeneVarByPoisson html modelGeneVarWithSpikes html multiMarkerStats html pairwiseBinom html pairwiseTTests html pairwiseWilcox html pseudoBulkDGE html pseudoBulkSpecific html quickCluster html quickSubCluster html rhoToPValue html sandbag html scaledColRanks html scoreMarkers html summaryMarkerStats html testLinearModel html ** 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 install for x64 * installing *source* package 'scran' ... ** libs "C:/rtools40/mingw64/bin/"g++ std=gnu++11 I"C:/Users/BIOCBU~1/BBS3~1.14/R/include" DNDEBUG I'C:/Users/biocbuild/bbs3.14bioc/R/library/Rcpp/include' I'C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include' I'C:/Users/biocbuild/bbs3.14bioc/R/library/BH/include' I'C:/Users/biocbuild/bbs3.14bioc/R/library/dqrng/include' I'C:/Users/biocbuild/bbs3.14bioc/R/library/scuttle/include' I"C:/extsoft/include" O2 Wall mfpmath=sse msse2 mstackrealign c RcppExports.cpp o RcppExports.o "C:/rtools40/mingw64/bin/"g++ std=gnu++11 I"C:/Users/BIOCBU~1/BBS3~1.14/R/include" DNDEBUG I'C:/Users/biocbuild/bbs3.14bioc/R/library/Rcpp/include' I'C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include' I'C:/Users/biocbuild/bbs3.14bioc/R/library/BH/include' I'C:/Users/biocbuild/bbs3.14bioc/R/library/dqrng/include' I'C:/Users/biocbuild/bbs3.14bioc/R/library/scuttle/include' I"C:/extsoft/include" O2 Wall mfpmath=sse msse2 mstackrealign c choose_effect_size.cpp o choose_effect_size.o choose_effect_size.cpp: In instantiation of 'size_t instantiate_list(Rcpp::List, std::vector<T>&, std::__cxx11::string) [with V = Rcpp::Vector<13>; size_t = long long unsigned int; Rcpp::List = Rcpp::Vector<19>; std::__cxx11::string = std::__cxx11::basic_string<char>]': choose_effect_size.cpp:38:67: required from here choose_effect_size.cpp:13:23: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long long unsigned int'} and 'R_xlen_t' {aka 'long long int'} [Wsigncompare] for (size_t c=0; c<input.size(); ++c) { ~^~~~~~~~~~~~~ choose_effect_size.cpp: In instantiation of 'size_t instantiate_list(Rcpp::List, std::vector<T>&, std::__cxx11::string) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; size_t = long long unsigned int; Rcpp::List = Rcpp::Vector<19>; std::__cxx11::string = std::__cxx11::basic_string<char>]': choose_effect_size.cpp:67:70: required from here choose_effect_size.cpp:13:23: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long long unsigned int'} and 'R_xlen_t' {aka 'long long int'} [Wsigncompare] "C:/rtools40/mingw64/bin/"g++ std=gnu++11 I"C:/Users/BIOCBU~1/BBS3~1.14/R/include" DNDEBUG I'C:/Users/biocbuild/bbs3.14bioc/R/library/Rcpp/include' I'C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include' I'C:/Users/biocbuild/bbs3.14bioc/R/library/BH/include' I'C:/Users/biocbuild/bbs3.14bioc/R/library/dqrng/include' I'C:/Users/biocbuild/bbs3.14bioc/R/library/scuttle/include' I"C:/extsoft/include" O2 Wall mfpmath=sse msse2 mstackrealign c combine_rho.cpp o combine_rho.o "C:/rtools40/mingw64/bin/"g++ std=gnu++11 I"C:/Users/BIOCBU~1/BBS3~1.14/R/include" DNDEBUG I'C:/Users/biocbuild/bbs3.14bioc/R/library/Rcpp/include' I'C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include' I'C:/Users/biocbuild/bbs3.14bioc/R/library/BH/include' I'C:/Users/biocbuild/bbs3.14bioc/R/library/dqrng/include' I'C:/Users/biocbuild/bbs3.14bioc/R/library/scuttle/include' I"C:/extsoft/include" O2 Wall mfpmath=sse msse2 mstackrealign c compute_blocked_stats.cpp o compute_blocked_stats.o In file included from C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:12, from C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:11, from C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/beachmat.h:24, from compute_blocked_stats.cpp:2: C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of 'beachmat::SparseArraySeed_reader<V, TIT>::SparseArraySeed_reader(Rcpp::RObject) [with V = Rcpp::Vector<13>; TIT = const int*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]': C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:561:56: required from 'beachmat::lin_SparseArraySeed<V, TIT>::lin_SparseArraySeed(Rcpp::RObject) [with V = Rcpp::Vector<13>; TIT = const int*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]' C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:36:39: required from 'std::unique_ptr<_Codecvt> beachmat::read_lin_sparse_block_raw(Rcpp::RObject) [with M = beachmat::lin_matrix; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]' C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:65:63: required from here C:/Users/biocbuild/bbs3.14bioc/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'} [Wsigncompare] if (nnz != x.size()) { C:/Users/biocbuild/bbs3.14bioc/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'} [Wsigncompare] if (lastR <= 0  lastR > NR  lastC <= 0  lastC > NC) { ~~~~~~^~~~ C:/Users/biocbuild/bbs3.14bioc/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'} [Wsigncompare] if (lastR <= 0  lastR > NR  lastC <= 0  lastC > NC) { ~~~~~~^~~~ C:/Users/biocbuild/bbs3.14bioc/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'} [Wsigncompare] for (int v = 0; v < nnz; ++v, ++rowIt, ++colIt, ++xIt) { ~~^~~~~ C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of 'beachmat::SparseArraySeed_reader<V, TIT>::SparseArraySeed_reader(Rcpp::RObject) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]': C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:561:56: required from 'beachmat::lin_SparseArraySeed<V, TIT>::lin_SparseArraySeed(Rcpp::RObject) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]' C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:38:39: required from 'std::unique_ptr<_Codecvt> beachmat::read_lin_sparse_block_raw(Rcpp::RObject) [with M = beachmat::lin_matrix; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]' C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:65:63: required from here C:/Users/biocbuild/bbs3.14bioc/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'} [Wsigncompare] if (nnz != x.size()) { C:/Users/biocbuild/bbs3.14bioc/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'} [Wsigncompare] if (lastR <= 0  lastR > NR  lastC <= 0  lastC > NC) { ~~~~~~^~~~ C:/Users/biocbuild/bbs3.14bioc/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'} [Wsigncompare] if (lastR <= 0  lastR > NR  lastC <= 0  lastC > NC) { ~~~~~~^~~~ C:/Users/biocbuild/bbs3.14bioc/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'} [Wsigncompare] for (int v = 0; v < nnz; ++v, ++rowIt, ++colIt, ++xIt) { ~~^~~~~ C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of 'beachmat::SparseArraySeed_reader<V, TIT>::SparseArraySeed_reader(Rcpp::RObject) [with V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]': C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:561:56: required from 'beachmat::lin_SparseArraySeed<V, TIT>::lin_SparseArraySeed(Rcpp::RObject) [with V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]' C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:40:39: required from 'std::unique_ptr<_Codecvt> beachmat::read_lin_sparse_block_raw(Rcpp::RObject) [with M = beachmat::lin_matrix; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]' C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:65:63: required from here C:/Users/biocbuild/bbs3.14bioc/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'} [Wsigncompare] if (nnz != x.size()) { C:/Users/biocbuild/bbs3.14bioc/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'} [Wsigncompare] if (lastR <= 0  lastR > NR  lastC <= 0  lastC > NC) { ~~~~~~^~~~ C:/Users/biocbuild/bbs3.14bioc/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'} [Wsigncompare] if (lastR <= 0  lastR > NR  lastC <= 0  lastC > NC) { ~~~~~~^~~~ C:/Users/biocbuild/bbs3.14bioc/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'} [Wsigncompare] for (int v = 0; v < nnz; ++v, ++rowIt, ++colIt, ++xIt) { ~~^~~~~ C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of 'beachmat::sparse_index<OUT, I> beachmat::Csparse_core<TIT, I, P>::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]': C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:650:73: required from 'beachmat::sparse_index<OUT, int> beachmat::SparseArraySeed_reader<V, TIT>::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]' C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:596:82: required from 'beachmat::sparse_index<const int*, int> beachmat::lin_SparseArraySeed<V, TIT>::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]' C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:595:35: required from here C:/Users/biocbuild/bbs3.14bioc/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' [Wsigncompare] if (idex != *pIt && static_cast<size_t>(i[idex]) == r) { ~~~~~^~~~~~~ C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of 'beachmat::sparse_index<OUT, I> beachmat::Csparse_core<TIT, I, P>::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]': C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:650:73: required from 'beachmat::sparse_index<OUT, int> beachmat::SparseArraySeed_reader<V, TIT>::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]' C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:602:85: required from 'beachmat::sparse_index<const double*, int> beachmat::lin_SparseArraySeed<V, TIT>::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]' C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:601:38: required from here C:/Users/biocbuild/bbs3.14bioc/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' [Wsigncompare] C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of 'beachmat::sparse_index<OUT, I> beachmat::Csparse_core<TIT, I, P>::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]': C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:650:73: required from 'beachmat::sparse_index<OUT, int> beachmat::SparseArraySeed_reader<V, TIT>::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]' C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:596:82: required from 'beachmat::sparse_index<const int*, int> beachmat::lin_SparseArraySeed<V, TIT>::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]' C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:595:35: required from here C:/Users/biocbuild/bbs3.14bioc/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' [Wsigncompare] C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of 'beachmat::sparse_index<OUT, I> beachmat::Csparse_core<TIT, I, P>::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]': C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:650:73: required from 'beachmat::sparse_index<OUT, int> beachmat::SparseArraySeed_reader<V, TIT>::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]' C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:602:85: required from 'beachmat::sparse_index<const double*, int> beachmat::lin_SparseArraySeed<V, TIT>::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]' C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:601:38: required from here C:/Users/biocbuild/bbs3.14bioc/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' [Wsigncompare] "C:/rtools40/mingw64/bin/"g++ std=gnu++11 I"C:/Users/BIOCBU~1/BBS3~1.14/R/include" DNDEBUG I'C:/Users/biocbuild/bbs3.14bioc/R/library/Rcpp/include' I'C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include' I'C:/Users/biocbuild/bbs3.14bioc/R/library/BH/include' I'C:/Users/biocbuild/bbs3.14bioc/R/library/dqrng/include' I'C:/Users/biocbuild/bbs3.14bioc/R/library/scuttle/include' I"C:/extsoft/include" O2 Wall mfpmath=sse msse2 mstackrealign c compute_residual_stats.cpp o compute_residual_stats.o In file included from C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:12, from C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:11, from C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/beachmat.h:24, from compute_residual_stats.cpp:2: C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of 'beachmat::SparseArraySeed_reader<V, TIT>::SparseArraySeed_reader(Rcpp::RObject) [with V = Rcpp::Vector<13>; TIT = const int*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]': C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:561:56: required from 'beachmat::lin_SparseArraySeed<V, TIT>::lin_SparseArraySeed(Rcpp::RObject) [with V = Rcpp::Vector<13>; TIT = const int*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]' C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:36:39: required from 'std::unique_ptr<_Codecvt> beachmat::read_lin_sparse_block_raw(Rcpp::RObject) [with M = beachmat::lin_matrix; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]' C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:65:63: required from here C:/Users/biocbuild/bbs3.14bioc/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'} [Wsigncompare] if (nnz != x.size()) { C:/Users/biocbuild/bbs3.14bioc/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'} [Wsigncompare] if (lastR <= 0  lastR > NR  lastC <= 0  lastC > NC) { ~~~~~~^~~~ C:/Users/biocbuild/bbs3.14bioc/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'} [Wsigncompare] if (lastR <= 0  lastR > NR  lastC <= 0  lastC > NC) { ~~~~~~^~~~ C:/Users/biocbuild/bbs3.14bioc/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'} [Wsigncompare] for (int v = 0; v < nnz; ++v, ++rowIt, ++colIt, ++xIt) { ~~^~~~~ C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of 'beachmat::SparseArraySeed_reader<V, TIT>::SparseArraySeed_reader(Rcpp::RObject) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]': C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:561:56: required from 'beachmat::lin_SparseArraySeed<V, TIT>::lin_SparseArraySeed(Rcpp::RObject) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]' C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:38:39: required from 'std::unique_ptr<_Codecvt> beachmat::read_lin_sparse_block_raw(Rcpp::RObject) [with M = beachmat::lin_matrix; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]' C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:65:63: required from here C:/Users/biocbuild/bbs3.14bioc/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'} [Wsigncompare] if (nnz != x.size()) { C:/Users/biocbuild/bbs3.14bioc/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'} [Wsigncompare] if (lastR <= 0  lastR > NR  lastC <= 0  lastC > NC) { ~~~~~~^~~~ C:/Users/biocbuild/bbs3.14bioc/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'} [Wsigncompare] if (lastR <= 0  lastR > NR  lastC <= 0  lastC > NC) { ~~~~~~^~~~ C:/Users/biocbuild/bbs3.14bioc/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'} [Wsigncompare] for (int v = 0; v < nnz; ++v, ++rowIt, ++colIt, ++xIt) { ~~^~~~~ C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of 'beachmat::SparseArraySeed_reader<V, TIT>::SparseArraySeed_reader(Rcpp::RObject) [with V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]': C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:561:56: required from 'beachmat::lin_SparseArraySeed<V, TIT>::lin_SparseArraySeed(Rcpp::RObject) [with V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]' C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:40:39: required from 'std::unique_ptr<_Codecvt> beachmat::read_lin_sparse_block_raw(Rcpp::RObject) [with M = beachmat::lin_matrix; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]' C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:65:63: required from here C:/Users/biocbuild/bbs3.14bioc/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'} [Wsigncompare] if (nnz != x.size()) { C:/Users/biocbuild/bbs3.14bioc/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'} [Wsigncompare] if (lastR <= 0  lastR > NR  lastC <= 0  lastC > NC) { ~~~~~~^~~~ C:/Users/biocbuild/bbs3.14bioc/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'} [Wsigncompare] if (lastR <= 0  lastR > NR  lastC <= 0  lastC > NC) { ~~~~~~^~~~ C:/Users/biocbuild/bbs3.14bioc/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'} [Wsigncompare] for (int v = 0; v < nnz; ++v, ++rowIt, ++colIt, ++xIt) { ~~^~~~~ C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of 'beachmat::sparse_index<OUT, I> beachmat::Csparse_core<TIT, I, P>::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]': C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:650:73: required from 'beachmat::sparse_index<OUT, int> beachmat::SparseArraySeed_reader<V, TIT>::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]' C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:596:82: required from 'beachmat::sparse_index<const int*, int> beachmat::lin_SparseArraySeed<V, TIT>::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]' C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:595:35: required from here C:/Users/biocbuild/bbs3.14bioc/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' [Wsigncompare] if (idex != *pIt && static_cast<size_t>(i[idex]) == r) { ~~~~~^~~~~~~ C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of 'beachmat::sparse_index<OUT, I> beachmat::Csparse_core<TIT, I, P>::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]': C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:650:73: required from 'beachmat::sparse_index<OUT, int> beachmat::SparseArraySeed_reader<V, TIT>::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]' C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:602:85: required from 'beachmat::sparse_index<const double*, int> beachmat::lin_SparseArraySeed<V, TIT>::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]' C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:601:38: required from here C:/Users/biocbuild/bbs3.14bioc/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' [Wsigncompare] C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of 'beachmat::sparse_index<OUT, I> beachmat::Csparse_core<TIT, I, P>::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]': C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:650:73: required from 'beachmat::sparse_index<OUT, int> beachmat::SparseArraySeed_reader<V, TIT>::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]' C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:596:82: required from 'beachmat::sparse_index<const int*, int> beachmat::lin_SparseArraySeed<V, TIT>::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]' C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:595:35: required from here C:/Users/biocbuild/bbs3.14bioc/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' [Wsigncompare] C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of 'beachmat::sparse_index<OUT, I> beachmat::Csparse_core<TIT, I, P>::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]': C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:650:73: required from 'beachmat::sparse_index<OUT, int> beachmat::SparseArraySeed_reader<V, TIT>::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]' C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:602:85: required from 'beachmat::sparse_index<const double*, int> beachmat::lin_SparseArraySeed<V, TIT>::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]' C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:601:38: required from here C:/Users/biocbuild/bbs3.14bioc/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' [Wsigncompare] "C:/rtools40/mingw64/bin/"g++ std=gnu++11 I"C:/Users/BIOCBU~1/BBS3~1.14/R/include" DNDEBUG I'C:/Users/biocbuild/bbs3.14bioc/R/library/Rcpp/include' I'C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include' I'C:/Users/biocbuild/bbs3.14bioc/R/library/BH/include' I'C:/Users/biocbuild/bbs3.14bioc/R/library/dqrng/include' I'C:/Users/biocbuild/bbs3.14bioc/R/library/scuttle/include' I"C:/extsoft/include" O2 Wall mfpmath=sse msse2 mstackrealign c compute_rho_null.cpp o compute_rho_null.o In file included from C:/Users/biocbuild/bbs3.14bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23, from C:/Users/biocbuild/bbs3.14bioc/R/library/BH/include/boost/mpl/arg.hpp:25, from C:/Users/biocbuild/bbs3.14bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24, from C:/Users/biocbuild/bbs3.14bioc/R/library/BH/include/boost/mpl/apply.hpp:24, from C:/Users/biocbuild/bbs3.14bioc/R/library/BH/include/boost/mpl/aux_/iter_apply.hpp:17, from C:/Users/biocbuild/bbs3.14bioc/R/library/BH/include/boost/mpl/aux_/find_if_pred.hpp:14, from C:/Users/biocbuild/bbs3.14bioc/R/library/BH/include/boost/mpl/find_if.hpp:17, from C:/Users/biocbuild/bbs3.14bioc/R/library/BH/include/boost/mpl/find.hpp:17, from C:/Users/biocbuild/bbs3.14bioc/R/library/BH/include/boost/mpl/aux_/contains_impl.hpp:20, from C:/Users/biocbuild/bbs3.14bioc/R/library/BH/include/boost/mpl/contains.hpp:20, from C:/Users/biocbuild/bbs3.14bioc/R/library/BH/include/boost/math/policies/policy.hpp:10, from C:/Users/biocbuild/bbs3.14bioc/R/library/BH/include/boost/math/special_functions/math_fwd.hpp:29, from C:/Users/biocbuild/bbs3.14bioc/R/library/BH/include/boost/math/special_functions/fpclassify.hpp:19, from C:/Users/biocbuild/bbs3.14bioc/R/library/BH/include/boost/random/hyperexponential_distribution.hpp:22, from C:/Users/biocbuild/bbs3.14bioc/R/library/BH/include/boost/random.hpp:69, from rand_custom.h:6, from compute_rho_null.cpp:3: C:/Users/biocbuild/bbs3.14bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [Wparentheses] failed ************ (Pred::************ ^ C:/Users/biocbuild/bbs3.14bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [Wparentheses] failed ************ (boost::mpl::not_<Pred>::************ ^ "C:/rtools40/mingw64/bin/"g++ std=gnu++11 I"C:/Users/BIOCBU~1/BBS3~1.14/R/include" DNDEBUG I'C:/Users/biocbuild/bbs3.14bioc/R/library/Rcpp/include' I'C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include' I'C:/Users/biocbuild/bbs3.14bioc/R/library/BH/include' I'C:/Users/biocbuild/bbs3.14bioc/R/library/dqrng/include' I'C:/Users/biocbuild/bbs3.14bioc/R/library/scuttle/include' I"C:/extsoft/include" O2 Wall mfpmath=sse msse2 mstackrealign c cyclone_scores.cpp o cyclone_scores.o In file included from C:/Users/biocbuild/bbs3.14bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23, from C:/Users/biocbuild/bbs3.14bioc/R/library/BH/include/boost/mpl/arg.hpp:25, from C:/Users/biocbuild/bbs3.14bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24, from C:/Users/biocbuild/bbs3.14bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16, from C:/Users/biocbuild/bbs3.14bioc/R/library/BH/include/boost/iterator/iterator_concepts.hpp:10, from C:/Users/biocbuild/bbs3.14bioc/R/library/BH/include/boost/range/concepts.hpp:20, from C:/Users/biocbuild/bbs3.14bioc/R/library/BH/include/boost/range/algorithm.hpp:29, from cyclone_scores.cpp:4: C:/Users/biocbuild/bbs3.14bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [Wparentheses] failed ************ (Pred::************ ^ C:/Users/biocbuild/bbs3.14bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [Wparentheses] failed ************ (boost::mpl::not_<Pred>::************ ^ In file included from C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:12, from C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:11, from C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/beachmat.h:24, from cyclone_scores.cpp:3: C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of 'beachmat::SparseArraySeed_reader<V, TIT>::SparseArraySeed_reader(Rcpp::RObject) [with V = Rcpp::Vector<13>; TIT = const int*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]': C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:561:56: required from 'beachmat::lin_SparseArraySeed<V, TIT>::lin_SparseArraySeed(Rcpp::RObject) [with V = Rcpp::Vector<13>; TIT = const int*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]' C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:36:39: required from 'std::unique_ptr<_Codecvt> beachmat::read_lin_sparse_block_raw(Rcpp::RObject) [with M = beachmat::lin_matrix; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]' C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:65:63: required from here C:/Users/biocbuild/bbs3.14bioc/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'} [Wsigncompare] if (nnz != x.size()) { C:/Users/biocbuild/bbs3.14bioc/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'} [Wsigncompare] if (lastR <= 0  lastR > NR  lastC <= 0  lastC > NC) { ~~~~~~^~~~ C:/Users/biocbuild/bbs3.14bioc/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'} [Wsigncompare] if (lastR <= 0  lastR > NR  lastC <= 0  lastC > NC) { ~~~~~~^~~~ C:/Users/biocbuild/bbs3.14bioc/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'} [Wsigncompare] for (int v = 0; v < nnz; ++v, ++rowIt, ++colIt, ++xIt) { ~~^~~~~ C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of 'beachmat::SparseArraySeed_reader<V, TIT>::SparseArraySeed_reader(Rcpp::RObject) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]': C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:561:56: required from 'beachmat::lin_SparseArraySeed<V, TIT>::lin_SparseArraySeed(Rcpp::RObject) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]' C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:38:39: required from 'std::unique_ptr<_Codecvt> beachmat::read_lin_sparse_block_raw(Rcpp::RObject) [with M = beachmat::lin_matrix; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]' C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:65:63: required from here C:/Users/biocbuild/bbs3.14bioc/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'} [Wsigncompare] if (nnz != x.size()) { C:/Users/biocbuild/bbs3.14bioc/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'} [Wsigncompare] if (lastR <= 0  lastR > NR  lastC <= 0  lastC > NC) { ~~~~~~^~~~ C:/Users/biocbuild/bbs3.14bioc/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'} [Wsigncompare] if (lastR <= 0  lastR > NR  lastC <= 0  lastC > NC) { ~~~~~~^~~~ C:/Users/biocbuild/bbs3.14bioc/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'} [Wsigncompare] for (int v = 0; v < nnz; ++v, ++rowIt, ++colIt, ++xIt) { ~~^~~~~ C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of 'beachmat::SparseArraySeed_reader<V, TIT>::SparseArraySeed_reader(Rcpp::RObject) [with V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]': C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:561:56: required from 'beachmat::lin_SparseArraySeed<V, TIT>::lin_SparseArraySeed(Rcpp::RObject) [with V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]' C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:40:39: required from 'std::unique_ptr<_Codecvt> beachmat::read_lin_sparse_block_raw(Rcpp::RObject) [with M = beachmat::lin_matrix; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]' C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:65:63: required from here C:/Users/biocbuild/bbs3.14bioc/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'} [Wsigncompare] if (nnz != x.size()) { C:/Users/biocbuild/bbs3.14bioc/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'} [Wsigncompare] if (lastR <= 0  lastR > NR  lastC <= 0  lastC > NC) { ~~~~~~^~~~ C:/Users/biocbuild/bbs3.14bioc/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'} [Wsigncompare] if (lastR <= 0  lastR > NR  lastC <= 0  lastC > NC) { ~~~~~~^~~~ C:/Users/biocbuild/bbs3.14bioc/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'} [Wsigncompare] for (int v = 0; v < nnz; ++v, ++rowIt, ++colIt, ++xIt) { ~~^~~~~ C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of 'beachmat::sparse_index<OUT, I> beachmat::Csparse_core<TIT, I, P>::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]': C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:650:73: required from 'beachmat::sparse_index<OUT, int> beachmat::SparseArraySeed_reader<V, TIT>::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]' C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:596:82: required from 'beachmat::sparse_index<const int*, int> beachmat::lin_SparseArraySeed<V, TIT>::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]' C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:595:35: required from here C:/Users/biocbuild/bbs3.14bioc/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' [Wsigncompare] if (idex != *pIt && static_cast<size_t>(i[idex]) == r) { ~~~~~^~~~~~~ C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of 'beachmat::sparse_index<OUT, I> beachmat::Csparse_core<TIT, I, P>::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]': C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:650:73: required from 'beachmat::sparse_index<OUT, int> beachmat::SparseArraySeed_reader<V, TIT>::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]' C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:602:85: required from 'beachmat::sparse_index<const double*, int> beachmat::lin_SparseArraySeed<V, TIT>::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]' C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:601:38: required from here C:/Users/biocbuild/bbs3.14bioc/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' [Wsigncompare] C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of 'beachmat::sparse_index<OUT, I> beachmat::Csparse_core<TIT, I, P>::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]': C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:650:73: required from 'beachmat::sparse_index<OUT, int> beachmat::SparseArraySeed_reader<V, TIT>::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]' C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:596:82: required from 'beachmat::sparse_index<const int*, int> beachmat::lin_SparseArraySeed<V, TIT>::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]' C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:595:35: required from here C:/Users/biocbuild/bbs3.14bioc/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' [Wsigncompare] C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of 'beachmat::sparse_index<OUT, I> beachmat::Csparse_core<TIT, I, P>::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]': C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:650:73: required from 'beachmat::sparse_index<OUT, int> beachmat::SparseArraySeed_reader<V, TIT>::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]' C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:602:85: required from 'beachmat::sparse_index<const double*, int> beachmat::lin_SparseArraySeed<V, TIT>::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]' C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:601:38: required from here C:/Users/biocbuild/bbs3.14bioc/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' [Wsigncompare] "C:/rtools40/mingw64/bin/"g++ std=gnu++11 I"C:/Users/BIOCBU~1/BBS3~1.14/R/include" DNDEBUG I'C:/Users/biocbuild/bbs3.14bioc/R/library/Rcpp/include' I'C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include' I'C:/Users/biocbuild/bbs3.14bioc/R/library/BH/include' I'C:/Users/biocbuild/bbs3.14bioc/R/library/dqrng/include' I'C:/Users/biocbuild/bbs3.14bioc/R/library/scuttle/include' I"C:/extsoft/include" O2 Wall mfpmath=sse msse2 mstackrealign c overlap_exprs.cpp o overlap_exprs.o overlap_exprs.cpp: In function 'Rcpp::NumericMatrix overlap_exprs_paired(Rcpp::RObject, Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::List, double)': overlap_exprs.cpp:214:27: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long long unsigned int'} and 'R_xlen_t' {aka 'long long int'} [Wsigncompare] for (size_t i=0; i<left.size(); ++i, ++oIt) { ~^~~~~~~~~~~~ overlap_exprs.cpp:202:18: warning: unused variable 'ngroups' [Wunusedvariable] const size_t ngroups=groups.size(); ^~~~~~~ In file included from C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:12, from C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:11, from C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/beachmat.h:24, from overlap_exprs.cpp:3: C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of 'beachmat::SparseArraySeed_reader<V, TIT>::SparseArraySeed_reader(Rcpp::RObject) [with V = Rcpp::Vector<13>; TIT = const int*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]': C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:561:56: required from 'beachmat::lin_SparseArraySeed<V, TIT>::lin_SparseArraySeed(Rcpp::RObject) [with V = Rcpp::Vector<13>; TIT = const int*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]' C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:36:39: required from 'std::unique_ptr<_Codecvt> beachmat::read_lin_sparse_block_raw(Rcpp::RObject) [with M = beachmat::lin_matrix; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]' C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:65:63: required from here C:/Users/biocbuild/bbs3.14bioc/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'} [Wsigncompare] if (nnz != x.size()) { C:/Users/biocbuild/bbs3.14bioc/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'} [Wsigncompare] if (lastR <= 0  lastR > NR  lastC <= 0  lastC > NC) { ~~~~~~^~~~ C:/Users/biocbuild/bbs3.14bioc/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'} [Wsigncompare] if (lastR <= 0  lastR > NR  lastC <= 0  lastC > NC) { ~~~~~~^~~~ C:/Users/biocbuild/bbs3.14bioc/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'} [Wsigncompare] for (int v = 0; v < nnz; ++v, ++rowIt, ++colIt, ++xIt) { ~~^~~~~ C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of 'beachmat::SparseArraySeed_reader<V, TIT>::SparseArraySeed_reader(Rcpp::RObject) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]': C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:561:56: required from 'beachmat::lin_SparseArraySeed<V, TIT>::lin_SparseArraySeed(Rcpp::RObject) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]' C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:38:39: required from 'std::unique_ptr<_Codecvt> beachmat::read_lin_sparse_block_raw(Rcpp::RObject) [with M = beachmat::lin_matrix; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]' C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:65:63: required from here C:/Users/biocbuild/bbs3.14bioc/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'} [Wsigncompare] if (nnz != x.size()) { C:/Users/biocbuild/bbs3.14bioc/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'} [Wsigncompare] if (lastR <= 0  lastR > NR  lastC <= 0  lastC > NC) { ~~~~~~^~~~ C:/Users/biocbuild/bbs3.14bioc/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'} [Wsigncompare] if (lastR <= 0  lastR > NR  lastC <= 0  lastC > NC) { ~~~~~~^~~~ C:/Users/biocbuild/bbs3.14bioc/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'} [Wsigncompare] for (int v = 0; v < nnz; ++v, ++rowIt, ++colIt, ++xIt) { ~~^~~~~ C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of 'beachmat::SparseArraySeed_reader<V, TIT>::SparseArraySeed_reader(Rcpp::RObject) [with V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]': C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:561:56: required from 'beachmat::lin_SparseArraySeed<V, TIT>::lin_SparseArraySeed(Rcpp::RObject) [with V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]' C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:40:39: required from 'std::unique_ptr<_Codecvt> beachmat::read_lin_sparse_block_raw(Rcpp::RObject) [with M = beachmat::lin_matrix; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]' C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:65:63: required from here C:/Users/biocbuild/bbs3.14bioc/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'} [Wsigncompare] if (nnz != x.size()) { C:/Users/biocbuild/bbs3.14bioc/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'} [Wsigncompare] if (lastR <= 0  lastR > NR  lastC <= 0  lastC > NC) { ~~~~~~^~~~ C:/Users/biocbuild/bbs3.14bioc/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'} [Wsigncompare] if (lastR <= 0  lastR > NR  lastC <= 0  lastC > NC) { ~~~~~~^~~~ C:/Users/biocbuild/bbs3.14bioc/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'} [Wsigncompare] for (int v = 0; v < nnz; ++v, ++rowIt, ++colIt, ++xIt) { ~~^~~~~ C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of 'beachmat::sparse_index<OUT, I> beachmat::Csparse_core<TIT, I, P>::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]': C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:650:73: required from 'beachmat::sparse_index<OUT, int> beachmat::SparseArraySeed_reader<V, TIT>::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]' C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:596:82: required from 'beachmat::sparse_index<const int*, int> beachmat::lin_SparseArraySeed<V, TIT>::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]' C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:595:35: required from here C:/Users/biocbuild/bbs3.14bioc/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' [Wsigncompare] if (idex != *pIt && static_cast<size_t>(i[idex]) == r) { ~~~~~^~~~~~~ C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of 'beachmat::sparse_index<OUT, I> beachmat::Csparse_core<TIT, I, P>::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]': C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:650:73: required from 'beachmat::sparse_index<OUT, int> beachmat::SparseArraySeed_reader<V, TIT>::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]' C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:602:85: required from 'beachmat::sparse_index<const double*, int> beachmat::lin_SparseArraySeed<V, TIT>::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]' C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:601:38: required from here C:/Users/biocbuild/bbs3.14bioc/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' [Wsigncompare] C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of 'beachmat::sparse_index<OUT, I> beachmat::Csparse_core<TIT, I, P>::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]': C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:650:73: required from 'beachmat::sparse_index<OUT, int> beachmat::SparseArraySeed_reader<V, TIT>::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]' C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:596:82: required from 'beachmat::sparse_index<const int*, int> beachmat::lin_SparseArraySeed<V, TIT>::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]' C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:595:35: required from here C:/Users/biocbuild/bbs3.14bioc/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' [Wsigncompare] C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of 'beachmat::sparse_index<OUT, I> beachmat::Csparse_core<TIT, I, P>::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]': C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:650:73: required from 'beachmat::sparse_index<OUT, int> beachmat::SparseArraySeed_reader<V, TIT>::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]' C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:602:85: required from 'beachmat::sparse_index<const double*, int> beachmat::lin_SparseArraySeed<V, TIT>::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]' C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:601:38: required from here C:/Users/biocbuild/bbs3.14bioc/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' [Wsigncompare] "C:/rtools40/mingw64/bin/"g++ std=gnu++11 I"C:/Users/BIOCBU~1/BBS3~1.14/R/include" DNDEBUG I'C:/Users/biocbuild/bbs3.14bioc/R/library/Rcpp/include' I'C:/Users/biocbuild/bbs3.14bioc/R/library/beachmat/include' I'C:/Users/biocbuild/bbs3.14bioc/R/library/BH/include' I'C:/Users/biocbuild/bbs3.14bioc/R/library/dqrng/include' I'C:/Users/biocbuild/bbs3.14bioc/R/library/scuttle/include' I"C:/extsoft/include" O2 Wall mfpmath=sse msse2 mstackrealign c rand_custom.cpp o rand_custom.o In file included from C:/Users/biocbuild/bbs3.14bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23, from C:/Users/biocbuild/bbs3.14bioc/R/library/BH/include/boost/mpl/arg.hpp:25, from C:/Users/biocbuild/bbs3.14bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24, from C:/Users/biocbuild/bbs3.14bioc/R/library/BH/include/boost/mpl/apply.hpp:24, from C:/Users/biocbuild/bbs3.14bioc/R/library/BH/include/boost/mpl/aux_/iter_apply.hpp:17, from C:/Users/biocbuild/bbs3.14bioc/R/library/BH/include/boost/mpl/aux_/find_if_pred.hpp:14, from C:/Users/biocbuild/bbs3.14bioc/R/library/BH/include/boost/mpl/find_if.hpp:17, from C:/Users/biocbuild/bbs3.14bioc/R/library/BH/include/boost/mpl/find.hpp:17, from C:/Users/biocbuild/bbs3.14bioc/R/library/BH/include/boost/mpl/aux_/contains_impl.hpp:20, from C:/Users/biocbuild/bbs3.14bioc/R/library/BH/include/boost/mpl/contains.hpp:20, from C:/Users/biocbuild/bbs3.14bioc/R/library/BH/include/boost/math/policies/policy.hpp:10, from C:/Users/biocbuild/bbs3.14bioc/R/library/BH/include/boost/math/special_functions/math_fwd.hpp:29, from C:/Users/biocbuild/bbs3.14bioc/R/library/BH/include/boost/math/special_functions/fpclassify.hpp:19, from C:/Users/biocbuild/bbs3.14bioc/R/library/BH/include/boost/random/hyperexponential_distribution.hpp:22, from C:/Users/biocbuild/bbs3.14bioc/R/library/BH/include/boost/random.hpp:69, from rand_custom.h:6, from rand_custom.cpp:1: C:/Users/biocbuild/bbs3.14bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [Wparentheses] failed ************ (Pred::************ ^ C:/Users/biocbuild/bbs3.14bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [Wparentheses] failed ************ (boost::mpl::not_<Pred>::************ ^ C:/rtools40/mingw64/bin/g++ shared s staticlibgcc o scran.dll tmp.def RcppExports.o choose_effect_size.o combine_rho.o compute_blocked_stats.o compute_residual_stats.o compute_rho_null.o cyclone_scores.o overlap_exprs.o rand_custom.o LC:/Users/BIOCBU~1/BBS3~1.14/R/bin/x64 lRlapack LC:/Users/BIOCBU~1/BBS3~1.14/R/bin/x64 lRblas lgfortran lm lquadmath LC:/extsoft/lib/x64 LC:/extsoft/lib LC:/Users/BIOCBU~1/BBS3~1.14/R/bin/x64 lR installing to C:/Users/biocbuild/bbs3.14bioc/meat/scran.buildbinlibdir/scran/libs/x64 ** testing if installed package can be loaded * MD5 sums packaged installation of 'scran' as scran_1.22.1.zip * DONE (scran) * installing to library 'C:/Users/biocbuild/bbs3.14bioc/R/library' package 'scran' successfully unpacked and MD5 sums checked
scran.Rcheck/tests_i386/testthat.Rout R version 4.1.2 (20211101)  "Bird Hippie" Copyright (C) 2021 The R Foundation for Statistical Computing Platform: i386w64mingw32/i386 (32bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for online help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library(testthat) > library(scran) Loading required package: SingleCellExperiment Loading required package: SummarizedExperiment Loading required package: MatrixGenerics Loading required package: matrixStats Attaching package: 'MatrixGenerics' The following objects are masked from 'package:matrixStats': colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse, colCounts, colCummaxs, colCummins, colCumprods, colCumsums, colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs, colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats, colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds, colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads, colWeightedMeans, colWeightedMedians, colWeightedSds, colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet, rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods, rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps, rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins, rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks, rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars, rowWeightedMads, rowWeightedMeans, rowWeightedMedians, rowWeightedSds, rowWeightedVars Loading required package: GenomicRanges Loading required package: stats4 Loading required package: BiocGenerics Attaching package: 'BiocGenerics' The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: S4Vectors Attaching package: 'S4Vectors' The following objects are masked from 'package:base': I, expand.grid, unname Loading required package: IRanges Attaching package: 'IRanges' The following object is masked from 'package:grDevices': windows Loading required package: GenomeInfoDb Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Attaching package: 'Biobase' The following object is masked from 'package:MatrixGenerics': rowMedians The following objects are masked from 'package:matrixStats': anyMissing, rowMedians Loading required package: scuttle > test_check("scran") Loading required package: Matrix Attaching package: 'Matrix' The following object is masked from 'package:S4Vectors': expand Attaching package: 'DelayedArray' The following objects are masked from 'package:base': aperm, apply, rowsum, scale, sweep == Skipped tests =============================================================== * On Windows (2) * monocle is a little broken because of clusterApply (1) [ FAIL 0  WARN 183  SKIP 3  PASS 4447 ] > > proc.time() user system elapsed 354.73 5.57 454.93 
scran.Rcheck/tests_x64/testthat.Rout R version 4.1.2 (20211101)  "Bird Hippie" Copyright (C) 2021 The R Foundation for Statistical Computing Platform: x86_64w64mingw32/x64 (64bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for online help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library(testthat) > library(scran) Loading required package: SingleCellExperiment Loading required package: SummarizedExperiment Loading required package: MatrixGenerics Loading required package: matrixStats Attaching package: 'MatrixGenerics' The following objects are masked from 'package:matrixStats': colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse, colCounts, colCummaxs, colCummins, colCumprods, colCumsums, colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs, colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats, colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds, colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads, colWeightedMeans, colWeightedMedians, colWeightedSds, colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet, rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods, rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps, rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins, rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks, rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars, rowWeightedMads, rowWeightedMeans, rowWeightedMedians, rowWeightedSds, rowWeightedVars Loading required package: GenomicRanges Loading required package: stats4 Loading required package: BiocGenerics Attaching package: 'BiocGenerics' The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: S4Vectors Attaching package: 'S4Vectors' The following objects are masked from 'package:base': I, expand.grid, unname Loading required package: IRanges Attaching package: 'IRanges' The following object is masked from 'package:grDevices': windows Loading required package: GenomeInfoDb Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Attaching package: 'Biobase' The following object is masked from 'package:MatrixGenerics': rowMedians The following objects are masked from 'package:matrixStats': anyMissing, rowMedians Loading required package: scuttle > test_check("scran") Loading required package: Matrix Attaching package: 'Matrix' The following object is masked from 'package:S4Vectors': expand Attaching package: 'DelayedArray' The following objects are masked from 'package:base': aperm, apply, rowsum, scale, sweep == Skipped tests =============================================================== * On Windows (2) * monocle is a little broken because of clusterApply (1) [ FAIL 0  WARN 183  SKIP 3  PASS 4447 ] > > proc.time() user system elapsed 395.31 2.78 544.56 
scran.Rcheck/examples_i386/scranEx.timings

scran.Rcheck/examples_x64/scranEx.timings
