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### Running command:
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### rm -rf beachmat.buildbin-libdir && mkdir beachmat.buildbin-libdir && C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.6/bioc/src/contrib/beachmat_1.0.2.tar.gz && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --library=beachmat.buildbin-libdir --merge-multiarch beachmat_1.0.2.tar.gz && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL beachmat_1.0.2.zip && rm beachmat_1.0.2.tar.gz beachmat_1.0.2.zip
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% 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 54656 100 54656 0 0 2277k 0 --:--:-- --:--:-- --:--:-- 2668k
install for i386
* installing *source* package 'beachmat' ...
** libs
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rhdf5lib/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c HDF5_utils.cpp -o HDF5_utils.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rhdf5lib/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c any_matrix.cpp -o any_matrix.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rhdf5lib/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c character_matrix.cpp -o character_matrix.o
In file included from Input_matrix.h:8:0,
from character_matrix.h:4,
from character_matrix.cpp:1:
simple_matrix.h: In instantiation of 'beachmat::simple_matrix<T, V>::simple_matrix(const RObject&) [with T = Rcpp::String; V = Rcpp::Vector<16>; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]':
character_matrix.cpp:30:95: required from here
simple_matrix.h:49:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (mat.size()!=(this->nrow)*NC) {
^
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rhdf5lib/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c character_output.cpp -o character_output.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rhdf5lib/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c find_chunks.cpp -o find_chunks.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rhdf5lib/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c functions.cpp -o functions.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rhdf5lib/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c integer_matrix.cpp -o integer_matrix.o
In file included from Input_matrix.h:8:0,
from LIN_matrix.h:4,
from integer_matrix.h:4,
from integer_matrix.cpp:1:
simple_matrix.h: In instantiation of 'beachmat::simple_matrix<T, V>::simple_matrix(const RObject&) [with T = int; V = Rcpp::Vector<13>; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]':
LIN_methods.h:116:96: required from 'beachmat::advanced_lin_matrix<T, V, M>::advanced_lin_matrix(const RObject&) [with T = int; V = Rcpp::Vector<13>; M = beachmat::simple_matrix<int, Rcpp::Vector<13> >; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]'
LIN_methods.h:178:121: required from 'beachmat::simple_lin_matrix<T, V>::simple_lin_matrix(const RObject&) [with T = int; V = Rcpp::Vector<13>; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]'
integer_matrix.cpp:37:78: required from here
simple_matrix.h:49:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (mat.size()!=(this->nrow)*NC) {
^
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rhdf5lib/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c logical_matrix.cpp -o logical_matrix.o
In file included from Input_matrix.h:11:0,
from LIN_matrix.h:4,
from logical_matrix.h:4,
from logical_matrix.cpp:1:
Psymm_matrix.h: In instantiation of 'beachmat::Psymm_matrix<T, V>::Psymm_matrix(const RObject&) [with T = int; V = Rcpp::Vector<10, Rcpp::PreserveStorage>; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]':
LIN_methods.h:116:96: required from 'beachmat::advanced_lin_matrix<T, V, M>::advanced_lin_matrix(const RObject&) [with T = int; V = Rcpp::Vector<10, Rcpp::PreserveStorage>; M = beachmat::Psymm_matrix<int, Rcpp::Vector<10, Rcpp::PreserveStorage> >; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]'
logical_matrix.cpp:39:85: required from here
Psymm_matrix.h:55:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (x.size()!=(NR*(NR+1))/2) { throw_custom_error("length of 'x' in a ", ctype, " object is inconsistent with its dimensions"); }
^
In file included from Input_matrix.h:9:0,
from LIN_matrix.h:4,
from logical_matrix.h:4,
from logical_matrix.cpp:1:
dense_matrix.h: In instantiation of 'beachmat::dense_matrix<T, V>::dense_matrix(const RObject&) [with T = int; V = Rcpp::Vector<10, Rcpp::PreserveStorage>; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]':
LIN_methods.h:116:96: required from 'beachmat::advanced_lin_matrix<T, V, M>::advanced_lin_matrix(const RObject&) [with T = int; V = Rcpp::Vector<10, Rcpp::PreserveStorage>; M = beachmat::dense_matrix<int, Rcpp::Vector<10, Rcpp::PreserveStorage> >; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]'
LIN_methods.h:194:118: required from 'beachmat::dense_lin_matrix<T, V>::dense_lin_matrix(const RObject&) [with T = int; V = Rcpp::Vector<10, Rcpp::PreserveStorage>; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]'
logical_matrix.cpp:33:85: required from here
dense_matrix.h:50:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (x.size()!=(this->nrow)*NC) {
^
In file included from Input_matrix.h:10:0,
from LIN_matrix.h:4,
from logical_matrix.h:4,
from logical_matrix.cpp:1:
Csparse_matrix.h: In instantiation of 'beachmat::Csparse_matrix<T, V>::Csparse_matrix(const RObject&) [with T = int; V = Rcpp::Vector<10, Rcpp::PreserveStorage>; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]':
LIN_methods.h:116:96: required from 'beachmat::advanced_lin_matrix<T, V, M>::advanced_lin_matrix(const RObject&) [with T = int; V = Rcpp::Vector<10, Rcpp::PreserveStorage>; M = beachmat::Csparse_matrix<int, Rcpp::Vector<10, Rcpp::PreserveStorage> >; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]'
LIN_methods.h:212:124: required from 'beachmat::Csparse_lin_matrix<T, V>::Csparse_lin_matrix(const RObject&) [with T = int; V = Rcpp::Vector<10, Rcpp::PreserveStorage>; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]'
logical_matrix.cpp:35:87: required from here
Csparse_matrix.h:72:13: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (NC+1!=p.size()) { throw_custom_error("length of 'p' slot in a ", ctype, " object should be equal to 'ncol+1'"); }
^
Csparse_matrix.h:101:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (curi<0 || curi>=NR) {
^
In file included from Input_matrix.h:8:0,
from LIN_matrix.h:4,
from logical_matrix.h:4,
from logical_matrix.cpp:1:
simple_matrix.h: In instantiation of 'beachmat::simple_matrix<T, V>::simple_matrix(const RObject&) [with T = int; V = Rcpp::Vector<10, Rcpp::PreserveStorage>; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]':
LIN_methods.h:116:96: required from 'beachmat::advanced_lin_matrix<T, V, M>::advanced_lin_matrix(const RObject&) [with T = int; V = Rcpp::Vector<10, Rcpp::PreserveStorage>; M = beachmat::simple_matrix<int, Rcpp::Vector<10, Rcpp::PreserveStorage> >; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]'
LIN_methods.h:178:121: required from 'beachmat::simple_lin_matrix<T, V>::simple_lin_matrix(const RObject&) [with T = int; V = Rcpp::Vector<10, Rcpp::PreserveStorage>; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]'
logical_matrix.cpp:53:78: required from here
simple_matrix.h:49:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (mat.size()!=(this->nrow)*NC) {
^
In file included from Input_matrix.h:10:0,
from LIN_matrix.h:4,
from logical_matrix.h:4,
from logical_matrix.cpp:1:
Csparse_matrix.h: In instantiation of 'void beachmat::Csparse_matrix<T, V>::get_row(size_t, Iter, size_t, size_t) [with Iter = int*; T = int; V = Rcpp::Vector<10, Rcpp::PreserveStorage>; size_t = unsigned int]':
LIN_methods.h:145:5: required from 'void beachmat::advanced_lin_matrix<T, V, M>::get_row(size_t, Rcpp::Vector<13>::iterator, size_t, size_t) [with T = int; V = Rcpp::Vector<10, Rcpp::PreserveStorage>; M = beachmat::Csparse_matrix<int, Rcpp::Vector<10, Rcpp::PreserveStorage> >; size_t = unsigned int; Rcpp::Vector<13>::iterator = int*; Rcpp::traits::storage_type<13>::type = int]'
logical_matrix.cpp:72:1: required from here
Csparse_matrix.h:199:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (idex!=*pIt && i[idex]==r) { (*out)=x[idex]; }
^
Csparse_matrix.h: In instantiation of 'void beachmat::Csparse_matrix<T, V>::get_row(size_t, Iter, size_t, size_t) [with Iter = double*; T = int; V = Rcpp::Vector<10, Rcpp::PreserveStorage>; size_t = unsigned int]':
LIN_methods.h:151:5: required from 'void beachmat::advanced_lin_matrix<T, V, M>::get_row(size_t, Rcpp::Vector<14, Rcpp::PreserveStorage>::iterator, size_t, size_t) [with T = int; V = Rcpp::Vector<10, Rcpp::PreserveStorage>; M = beachmat::Csparse_matrix<int, Rcpp::Vector<10, Rcpp::PreserveStorage> >; size_t = unsigned int; Rcpp::Vector<14, Rcpp::PreserveStorage>::iterator = double*; Rcpp::traits::storage_type<14>::type = double]'
logical_matrix.cpp:72:1: required from here
Csparse_matrix.h:199:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Csparse_matrix.h: In instantiation of 'T beachmat::Csparse_matrix<T, V>::get(size_t, size_t) [with T = int; V = Rcpp::Vector<10, Rcpp::PreserveStorage>; size_t = unsigned int]':
LIN_methods.h:157:24: required from 'T beachmat::advanced_lin_matrix<T, V, M>::get(size_t, size_t) [with T = int; V = Rcpp::Vector<10, Rcpp::PreserveStorage>; M = beachmat::Csparse_matrix<int, Rcpp::Vector<10, Rcpp::PreserveStorage> >; size_t = unsigned int]'
logical_matrix.cpp:72:1: required from here
Csparse_matrix.h:119:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (loc!=iend && *loc==r) {
^
Csparse_matrix.h: In instantiation of 'size_t beachmat::Csparse_matrix<T, V>::get_nonzero_row(size_t, Rcpp::Vector<13>::iterator, Iter, size_t, size_t) [with Iter = int*; T = int; V = Rcpp::Vector<10, Rcpp::PreserveStorage>; size_t = unsigned int; Rcpp::Vector<13>::iterator = int*; Rcpp::traits::storage_type<13>::type = int]':
LIN_methods.h:229:62: required from 'size_t beachmat::Csparse_lin_matrix<T, V>::get_nonzero_row(size_t, Rcpp::Vector<13>::iterator, Rcpp::Vector<13>::iterator, size_t, size_t) [with T = int; V = Rcpp::Vector<10, Rcpp::PreserveStorage>; size_t = unsigned int; Rcpp::Vector<13>::iterator = int*; Rcpp::traits::storage_type<13>::type = int]'
logical_matrix.cpp:72:1: required from here
Csparse_matrix.h:239:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (idex!=*pIt && i[idex]==r) {
^
Csparse_matrix.h: In instantiation of 'size_t beachmat::Csparse_matrix<T, V>::get_nonzero_row(size_t, Rcpp::Vector<13>::iterator, Iter, size_t, size_t) [with Iter = double*; T = int; V = Rcpp::Vector<10, Rcpp::PreserveStorage>; size_t = unsigned int; Rcpp::Vector<13>::iterator = int*; Rcpp::traits::storage_type<13>::type = int]':
LIN_methods.h:234:62: required from 'size_t beachmat::Csparse_lin_matrix<T, V>::get_nonzero_row(size_t, Rcpp::Vector<13>::iterator, Rcpp::Vector<14, Rcpp::PreserveStorage>::iterator, size_t, size_t) [with T = int; V = Rcpp::Vector<10, Rcpp::PreserveStorage>; size_t = unsigned int; Rcpp::Vector<13>::iterator = int*; Rcpp::traits::storage_type<13>::type = int; Rcpp::Vector<14, Rcpp::PreserveStorage>::iterator = double*; Rcpp::traits::storage_type<14>::type = double]'
logical_matrix.cpp:72:1: required from here
Csparse_matrix.h:239:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Csparse_matrix.h: In instantiation of 'void beachmat::Csparse_matrix<T, V>::update_indices(size_t, size_t, size_t) [with T = int; V = Rcpp::Vector<10, Rcpp::PreserveStorage>; size_t = unsigned int]':
Csparse_matrix.h:193:34: required from 'void beachmat::Csparse_matrix<T, V>::get_row(size_t, Iter, size_t, size_t) [with Iter = int*; T = int; V = Rcpp::Vector<10, Rcpp::PreserveStorage>; size_t = unsigned int]'
LIN_methods.h:145:5: required from 'void beachmat::advanced_lin_matrix<T, V, M>::get_row(size_t, Rcpp::Vector<13>::iterator, size_t, size_t) [with T = int; V = Rcpp::Vector<10, Rcpp::PreserveStorage>; M = beachmat::Csparse_matrix<int, Rcpp::Vector<10, Rcpp::PreserveStorage> >; size_t = unsigned int; Rcpp::Vector<13>::iterator = int*; Rcpp::traits::storage_type<13>::type = int]'
logical_matrix.cpp:72:1: required from here
Csparse_matrix.h:155:43: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (curdex!=*pIt && i[curdex] < r) {
^
Csparse_matrix.h:162:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (curdex!=*pIt && i[curdex-1] >= r) {
^
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rhdf5lib/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c numeric_matrix.cpp -o numeric_matrix.o
In file included from Input_matrix.h:11:0,
from LIN_matrix.h:4,
from numeric_matrix.h:4,
from numeric_matrix.cpp:1:
Psymm_matrix.h: In instantiation of 'beachmat::Psymm_matrix<T, V>::Psymm_matrix(const RObject&) [with T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]':
LIN_methods.h:116:96: required from 'beachmat::advanced_lin_matrix<T, V, M>::advanced_lin_matrix(const RObject&) [with T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; M = beachmat::Psymm_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]'
numeric_matrix.cpp:39:85: required from here
Psymm_matrix.h:55:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (x.size()!=(NR*(NR+1))/2) { throw_custom_error("length of 'x' in a ", ctype, " object is inconsistent with its dimensions"); }
^
In file included from Input_matrix.h:9:0,
from LIN_matrix.h:4,
from numeric_matrix.h:4,
from numeric_matrix.cpp:1:
dense_matrix.h: In instantiation of 'beachmat::dense_matrix<T, V>::dense_matrix(const RObject&) [with T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]':
LIN_methods.h:116:96: required from 'beachmat::advanced_lin_matrix<T, V, M>::advanced_lin_matrix(const RObject&) [with T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; M = beachmat::dense_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]'
LIN_methods.h:194:118: required from 'beachmat::dense_lin_matrix<T, V>::dense_lin_matrix(const RObject&) [with T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]'
numeric_matrix.cpp:33:85: required from here
dense_matrix.h:50:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (x.size()!=(this->nrow)*NC) {
^
In file included from Input_matrix.h:10:0,
from LIN_matrix.h:4,
from numeric_matrix.h:4,
from numeric_matrix.cpp:1:
Csparse_matrix.h: In instantiation of 'beachmat::Csparse_matrix<T, V>::Csparse_matrix(const RObject&) [with T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]':
LIN_methods.h:116:96: required from 'beachmat::advanced_lin_matrix<T, V, M>::advanced_lin_matrix(const RObject&) [with T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; M = beachmat::Csparse_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]'
LIN_methods.h:212:124: required from 'beachmat::Csparse_lin_matrix<T, V>::Csparse_lin_matrix(const RObject&) [with T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]'
numeric_matrix.cpp:35:87: required from here
Csparse_matrix.h:72:13: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (NC+1!=p.size()) { throw_custom_error("length of 'p' slot in a ", ctype, " object should be equal to 'ncol+1'"); }
^
Csparse_matrix.h:101:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (curi<0 || curi>=NR) {
^
In file included from Input_matrix.h:8:0,
from LIN_matrix.h:4,
from numeric_matrix.h:4,
from numeric_matrix.cpp:1:
simple_matrix.h: In instantiation of 'beachmat::simple_matrix<T, V>::simple_matrix(const RObject&) [with T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]':
LIN_methods.h:116:96: required from 'beachmat::advanced_lin_matrix<T, V, M>::advanced_lin_matrix(const RObject&) [with T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; M = beachmat::simple_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]'
LIN_methods.h:178:121: required from 'beachmat::simple_lin_matrix<T, V>::simple_lin_matrix(const RObject&) [with T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]'
numeric_matrix.cpp:53:78: required from here
simple_matrix.h:49:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (mat.size()!=(this->nrow)*NC) {
^
In file included from Input_matrix.h:10:0,
from LIN_matrix.h:4,
from numeric_matrix.h:4,
from numeric_matrix.cpp:1:
Csparse_matrix.h: In instantiation of 'void beachmat::Csparse_matrix<T, V>::get_row(size_t, Iter, size_t, size_t) [with Iter = int*; T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; size_t = unsigned int]':
LIN_methods.h:145:5: required from 'void beachmat::advanced_lin_matrix<T, V, M>::get_row(size_t, Rcpp::Vector<13>::iterator, size_t, size_t) [with T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; M = beachmat::Csparse_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >; size_t = unsigned int; Rcpp::Vector<13>::iterator = int*; Rcpp::traits::storage_type<13>::type = int]'
numeric_matrix.cpp:72:1: required from here
Csparse_matrix.h:199:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (idex!=*pIt && i[idex]==r) { (*out)=x[idex]; }
^
Csparse_matrix.h: In instantiation of 'void beachmat::Csparse_matrix<T, V>::get_row(size_t, Iter, size_t, size_t) [with Iter = double*; T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; size_t = unsigned int]':
LIN_methods.h:151:5: required from 'void beachmat::advanced_lin_matrix<T, V, M>::get_row(size_t, Rcpp::Vector<14, Rcpp::PreserveStorage>::iterator, size_t, size_t) [with T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; M = beachmat::Csparse_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >; size_t = unsigned int; Rcpp::Vector<14, Rcpp::PreserveStorage>::iterator = double*; Rcpp::traits::storage_type<14>::type = double]'
numeric_matrix.cpp:72:1: required from here
Csparse_matrix.h:199:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Csparse_matrix.h: In instantiation of 'T beachmat::Csparse_matrix<T, V>::get(size_t, size_t) [with T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; size_t = unsigned int]':
LIN_methods.h:157:24: required from 'T beachmat::advanced_lin_matrix<T, V, M>::get(size_t, size_t) [with T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; M = beachmat::Csparse_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >; size_t = unsigned int]'
numeric_matrix.cpp:72:1: required from here
Csparse_matrix.h:119:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (loc!=iend && *loc==r) {
^
Csparse_matrix.h: In instantiation of 'size_t beachmat::Csparse_matrix<T, V>::get_nonzero_row(size_t, Rcpp::Vector<13>::iterator, Iter, size_t, size_t) [with Iter = int*; T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; size_t = unsigned int; Rcpp::Vector<13>::iterator = int*; Rcpp::traits::storage_type<13>::type = int]':
LIN_methods.h:229:62: required from 'size_t beachmat::Csparse_lin_matrix<T, V>::get_nonzero_row(size_t, Rcpp::Vector<13>::iterator, Rcpp::Vector<13>::iterator, size_t, size_t) [with T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; size_t = unsigned int; Rcpp::Vector<13>::iterator = int*; Rcpp::traits::storage_type<13>::type = int]'
numeric_matrix.cpp:72:1: required from here
Csparse_matrix.h:239:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (idex!=*pIt && i[idex]==r) {
^
Csparse_matrix.h: In instantiation of 'size_t beachmat::Csparse_matrix<T, V>::get_nonzero_row(size_t, Rcpp::Vector<13>::iterator, Iter, size_t, size_t) [with Iter = double*; T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; size_t = unsigned int; Rcpp::Vector<13>::iterator = int*; Rcpp::traits::storage_type<13>::type = int]':
LIN_methods.h:234:62: required from 'size_t beachmat::Csparse_lin_matrix<T, V>::get_nonzero_row(size_t, Rcpp::Vector<13>::iterator, Rcpp::Vector<14, Rcpp::PreserveStorage>::iterator, size_t, size_t) [with T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; size_t = unsigned int; Rcpp::Vector<13>::iterator = int*; Rcpp::traits::storage_type<13>::type = int; Rcpp::Vector<14, Rcpp::PreserveStorage>::iterator = double*; Rcpp::traits::storage_type<14>::type = double]'
numeric_matrix.cpp:72:1: required from here
Csparse_matrix.h:239:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Csparse_matrix.h: In instantiation of 'void beachmat::Csparse_matrix<T, V>::update_indices(size_t, size_t, size_t) [with T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; size_t = unsigned int]':
Csparse_matrix.h:193:34: required from 'void beachmat::Csparse_matrix<T, V>::get_row(size_t, Iter, size_t, size_t) [with Iter = int*; T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; size_t = unsigned int]'
LIN_methods.h:145:5: required from 'void beachmat::advanced_lin_matrix<T, V, M>::get_row(size_t, Rcpp::Vector<13>::iterator, size_t, size_t) [with T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; M = beachmat::Csparse_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >; size_t = unsigned int; Rcpp::Vector<13>::iterator = int*; Rcpp::traits::storage_type<13>::type = int]'
numeric_matrix.cpp:72:1: required from here
Csparse_matrix.h:155:43: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (curdex!=*pIt && i[curdex] < r) {
^
Csparse_matrix.h:162:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (curdex!=*pIt && i[curdex-1] >= r) {
^
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rhdf5lib/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c output_param.cpp -o output_param.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rhdf5lib/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c repacker.cpp -o repacker.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rhdf5lib/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c utils.cpp -o utils.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o beachmat.dll tmp.def HDF5_utils.o any_matrix.o character_matrix.o character_output.o find_chunks.o functions.o integer_matrix.o logical_matrix.o numeric_matrix.o output_param.o repacker.o utils.o -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/library/Rhdf5lib/lib/i386 -lhdf5_cpp -lhdf5 -lszip -lz -lpsapi -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/i386 -lR -lm -LC:/local323/lib/i386 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/i386 -lR
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o libbeachmat.dll any_matrix.o character_matrix.o character_output.o integer_matrix.o logical_matrix.o numeric_matrix.o utils.o HDF5_utils.o output_param.o -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/library/Rhdf5lib/lib/i386 -lhdf5_cpp -lhdf5 -lszip -lz -lpsapi -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/i386 -lR -lm
C:/Rtools/mingw_32/bin/ar crs libbeachmat.a any_matrix.o character_matrix.o character_output.o integer_matrix.o logical_matrix.o numeric_matrix.o utils.o HDF5_utils.o output_param.o
mkdir -p "C:/Users/biocbuild/bbs-3.6-bioc/meat/beachmat.buildbin-libdir/beachmat/lib/i386" "C:/Users/biocbuild/bbs-3.6-bioc/meat/beachmat.buildbin-libdir/beachmat/include/beachmat"
cp any_matrix.h utils.h beachmat.h HDF5_utils.h output_param.h Psymm_matrix.h HDF5_matrix.h Csparse_matrix.h dense_matrix.h simple_matrix.h Rle_matrix.h Input_matrix.h simple_output.h Csparse_output.h HDF5_output.h Output_matrix.h LIN_matrix.h LIN_methods.h LIN_output.h LIN_outfun.h logical_matrix.h integer_matrix.h character_matrix.h numeric_matrix.h character_output.h "C:/Users/biocbuild/bbs-3.6-bioc/meat/beachmat.buildbin-libdir/beachmat/include/beachmat"
mv libbeachmat.* "C:/Users/biocbuild/bbs-3.6-bioc/meat/beachmat.buildbin-libdir/beachmat/lib/i386"
installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/beachmat.buildbin-libdir/beachmat/libs/i386
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
converting help for package 'beachmat'
finding HTML links ... done
getBestChunkDims html
pkgconfig html
rechunkByMargins html
finding level-2 HTML links ... done
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'beachmat' ...
** libs
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rhdf5lib/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c HDF5_utils.cpp -o HDF5_utils.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rhdf5lib/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c any_matrix.cpp -o any_matrix.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rhdf5lib/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c character_matrix.cpp -o character_matrix.o
In file included from Input_matrix.h:8:0,
from character_matrix.h:4,
from character_matrix.cpp:1:
simple_matrix.h: In instantiation of 'beachmat::simple_matrix<T, V>::simple_matrix(const RObject&) [with T = Rcpp::String; V = Rcpp::Vector<16>; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]':
character_matrix.cpp:30:95: required from here
simple_matrix.h:49:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (mat.size()!=(this->nrow)*NC) {
^
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rhdf5lib/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c character_output.cpp -o character_output.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rhdf5lib/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c find_chunks.cpp -o find_chunks.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rhdf5lib/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c functions.cpp -o functions.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rhdf5lib/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c integer_matrix.cpp -o integer_matrix.o
In file included from Input_matrix.h:8:0,
from LIN_matrix.h:4,
from integer_matrix.h:4,
from integer_matrix.cpp:1:
simple_matrix.h: In instantiation of 'beachmat::simple_matrix<T, V>::simple_matrix(const RObject&) [with T = int; V = Rcpp::Vector<13>; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]':
LIN_methods.h:116:96: required from 'beachmat::advanced_lin_matrix<T, V, M>::advanced_lin_matrix(const RObject&) [with T = int; V = Rcpp::Vector<13>; M = beachmat::simple_matrix<int, Rcpp::Vector<13> >; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]'
LIN_methods.h:178:121: required from 'beachmat::simple_lin_matrix<T, V>::simple_lin_matrix(const RObject&) [with T = int; V = Rcpp::Vector<13>; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]'
integer_matrix.cpp:37:78: required from here
simple_matrix.h:49:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (mat.size()!=(this->nrow)*NC) {
^
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rhdf5lib/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c logical_matrix.cpp -o logical_matrix.o
In file included from Input_matrix.h:11:0,
from LIN_matrix.h:4,
from logical_matrix.h:4,
from logical_matrix.cpp:1:
Psymm_matrix.h: In instantiation of 'beachmat::Psymm_matrix<T, V>::Psymm_matrix(const RObject&) [with T = int; V = Rcpp::Vector<10, Rcpp::PreserveStorage>; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]':
LIN_methods.h:116:96: required from 'beachmat::advanced_lin_matrix<T, V, M>::advanced_lin_matrix(const RObject&) [with T = int; V = Rcpp::Vector<10, Rcpp::PreserveStorage>; M = beachmat::Psymm_matrix<int, Rcpp::Vector<10, Rcpp::PreserveStorage> >; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]'
logical_matrix.cpp:39:85: required from here
Psymm_matrix.h:55:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (x.size()!=(NR*(NR+1))/2) { throw_custom_error("length of 'x' in a ", ctype, " object is inconsistent with its dimensions"); }
^
In file included from Input_matrix.h:9:0,
from LIN_matrix.h:4,
from logical_matrix.h:4,
from logical_matrix.cpp:1:
dense_matrix.h: In instantiation of 'beachmat::dense_matrix<T, V>::dense_matrix(const RObject&) [with T = int; V = Rcpp::Vector<10, Rcpp::PreserveStorage>; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]':
LIN_methods.h:116:96: required from 'beachmat::advanced_lin_matrix<T, V, M>::advanced_lin_matrix(const RObject&) [with T = int; V = Rcpp::Vector<10, Rcpp::PreserveStorage>; M = beachmat::dense_matrix<int, Rcpp::Vector<10, Rcpp::PreserveStorage> >; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]'
LIN_methods.h:194:118: required from 'beachmat::dense_lin_matrix<T, V>::dense_lin_matrix(const RObject&) [with T = int; V = Rcpp::Vector<10, Rcpp::PreserveStorage>; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]'
logical_matrix.cpp:33:85: required from here
dense_matrix.h:50:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (x.size()!=(this->nrow)*NC) {
^
In file included from Input_matrix.h:10:0,
from LIN_matrix.h:4,
from logical_matrix.h:4,
from logical_matrix.cpp:1:
Csparse_matrix.h: In instantiation of 'beachmat::Csparse_matrix<T, V>::Csparse_matrix(const RObject&) [with T = int; V = Rcpp::Vector<10, Rcpp::PreserveStorage>; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]':
LIN_methods.h:116:96: required from 'beachmat::advanced_lin_matrix<T, V, M>::advanced_lin_matrix(const RObject&) [with T = int; V = Rcpp::Vector<10, Rcpp::PreserveStorage>; M = beachmat::Csparse_matrix<int, Rcpp::Vector<10, Rcpp::PreserveStorage> >; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]'
LIN_methods.h:212:124: required from 'beachmat::Csparse_lin_matrix<T, V>::Csparse_lin_matrix(const RObject&) [with T = int; V = Rcpp::Vector<10, Rcpp::PreserveStorage>; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]'
logical_matrix.cpp:35:87: required from here
Csparse_matrix.h:72:13: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (NC+1!=p.size()) { throw_custom_error("length of 'p' slot in a ", ctype, " object should be equal to 'ncol+1'"); }
^
Csparse_matrix.h:101:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (curi<0 || curi>=NR) {
^
In file included from Input_matrix.h:8:0,
from LIN_matrix.h:4,
from logical_matrix.h:4,
from logical_matrix.cpp:1:
simple_matrix.h: In instantiation of 'beachmat::simple_matrix<T, V>::simple_matrix(const RObject&) [with T = int; V = Rcpp::Vector<10, Rcpp::PreserveStorage>; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]':
LIN_methods.h:116:96: required from 'beachmat::advanced_lin_matrix<T, V, M>::advanced_lin_matrix(const RObject&) [with T = int; V = Rcpp::Vector<10, Rcpp::PreserveStorage>; M = beachmat::simple_matrix<int, Rcpp::Vector<10, Rcpp::PreserveStorage> >; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]'
LIN_methods.h:178:121: required from 'beachmat::simple_lin_matrix<T, V>::simple_lin_matrix(const RObject&) [with T = int; V = Rcpp::Vector<10, Rcpp::PreserveStorage>; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]'
logical_matrix.cpp:53:78: required from here
simple_matrix.h:49:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (mat.size()!=(this->nrow)*NC) {
^
In file included from Input_matrix.h:10:0,
from LIN_matrix.h:4,
from logical_matrix.h:4,
from logical_matrix.cpp:1:
Csparse_matrix.h: In instantiation of 'void beachmat::Csparse_matrix<T, V>::get_row(size_t, Iter, size_t, size_t) [with Iter = int*; T = int; V = Rcpp::Vector<10, Rcpp::PreserveStorage>; size_t = long long unsigned int]':
LIN_methods.h:145:5: required from 'void beachmat::advanced_lin_matrix<T, V, M>::get_row(size_t, Rcpp::Vector<13>::iterator, size_t, size_t) [with T = int; V = Rcpp::Vector<10, Rcpp::PreserveStorage>; M = beachmat::Csparse_matrix<int, Rcpp::Vector<10, Rcpp::PreserveStorage> >; size_t = long long unsigned int; Rcpp::Vector<13>::iterator = int*; Rcpp::traits::storage_type<13>::type = int]'
logical_matrix.cpp:72:1: required from here
Csparse_matrix.h:199:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (idex!=*pIt && i[idex]==r) { (*out)=x[idex]; }
^
Csparse_matrix.h: In instantiation of 'void beachmat::Csparse_matrix<T, V>::get_row(size_t, Iter, size_t, size_t) [with Iter = double*; T = int; V = Rcpp::Vector<10, Rcpp::PreserveStorage>; size_t = long long unsigned int]':
LIN_methods.h:151:5: required from 'void beachmat::advanced_lin_matrix<T, V, M>::get_row(size_t, Rcpp::Vector<14, Rcpp::PreserveStorage>::iterator, size_t, size_t) [with T = int; V = Rcpp::Vector<10, Rcpp::PreserveStorage>; M = beachmat::Csparse_matrix<int, Rcpp::Vector<10, Rcpp::PreserveStorage> >; size_t = long long unsigned int; Rcpp::Vector<14, Rcpp::PreserveStorage>::iterator = double*; Rcpp::traits::storage_type<14>::type = double]'
logical_matrix.cpp:72:1: required from here
Csparse_matrix.h:199:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Csparse_matrix.h: In instantiation of 'T beachmat::Csparse_matrix<T, V>::get(size_t, size_t) [with T = int; V = Rcpp::Vector<10, Rcpp::PreserveStorage>; size_t = long long unsigned int]':
LIN_methods.h:157:24: required from 'T beachmat::advanced_lin_matrix<T, V, M>::get(size_t, size_t) [with T = int; V = Rcpp::Vector<10, Rcpp::PreserveStorage>; M = beachmat::Csparse_matrix<int, Rcpp::Vector<10, Rcpp::PreserveStorage> >; size_t = long long unsigned int]'
logical_matrix.cpp:72:1: required from here
Csparse_matrix.h:119:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (loc!=iend && *loc==r) {
^
Csparse_matrix.h: In instantiation of 'size_t beachmat::Csparse_matrix<T, V>::get_nonzero_row(size_t, Rcpp::Vector<13>::iterator, Iter, size_t, size_t) [with Iter = int*; T = int; V = Rcpp::Vector<10, Rcpp::PreserveStorage>; size_t = long long unsigned int; Rcpp::Vector<13>::iterator = int*; Rcpp::traits::storage_type<13>::type = int]':
LIN_methods.h:229:62: required from 'size_t beachmat::Csparse_lin_matrix<T, V>::get_nonzero_row(size_t, Rcpp::Vector<13>::iterator, Rcpp::Vector<13>::iterator, size_t, size_t) [with T = int; V = Rcpp::Vector<10, Rcpp::PreserveStorage>; size_t = long long unsigned int; Rcpp::Vector<13>::iterator = int*; Rcpp::traits::storage_type<13>::type = int]'
logical_matrix.cpp:72:1: required from here
Csparse_matrix.h:239:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (idex!=*pIt && i[idex]==r) {
^
Csparse_matrix.h: In instantiation of 'size_t beachmat::Csparse_matrix<T, V>::get_nonzero_row(size_t, Rcpp::Vector<13>::iterator, Iter, size_t, size_t) [with Iter = double*; T = int; V = Rcpp::Vector<10, Rcpp::PreserveStorage>; size_t = long long unsigned int; Rcpp::Vector<13>::iterator = int*; Rcpp::traits::storage_type<13>::type = int]':
LIN_methods.h:234:62: required from 'size_t beachmat::Csparse_lin_matrix<T, V>::get_nonzero_row(size_t, Rcpp::Vector<13>::iterator, Rcpp::Vector<14, Rcpp::PreserveStorage>::iterator, size_t, size_t) [with T = int; V = Rcpp::Vector<10, Rcpp::PreserveStorage>; size_t = long long unsigned int; Rcpp::Vector<13>::iterator = int*; Rcpp::traits::storage_type<13>::type = int; Rcpp::Vector<14, Rcpp::PreserveStorage>::iterator = double*; Rcpp::traits::storage_type<14>::type = double]'
logical_matrix.cpp:72:1: required from here
Csparse_matrix.h:239:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Csparse_matrix.h: In instantiation of 'void beachmat::Csparse_matrix<T, V>::update_indices(size_t, size_t, size_t) [with T = int; V = Rcpp::Vector<10, Rcpp::PreserveStorage>; size_t = long long unsigned int]':
Csparse_matrix.h:193:34: required from 'void beachmat::Csparse_matrix<T, V>::get_row(size_t, Iter, size_t, size_t) [with Iter = int*; T = int; V = Rcpp::Vector<10, Rcpp::PreserveStorage>; size_t = long long unsigned int]'
LIN_methods.h:145:5: required from 'void beachmat::advanced_lin_matrix<T, V, M>::get_row(size_t, Rcpp::Vector<13>::iterator, size_t, size_t) [with T = int; V = Rcpp::Vector<10, Rcpp::PreserveStorage>; M = beachmat::Csparse_matrix<int, Rcpp::Vector<10, Rcpp::PreserveStorage> >; size_t = long long unsigned int; Rcpp::Vector<13>::iterator = int*; Rcpp::traits::storage_type<13>::type = int]'
logical_matrix.cpp:72:1: required from here
Csparse_matrix.h:155:43: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (curdex!=*pIt && i[curdex] < r) {
^
Csparse_matrix.h:162:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (curdex!=*pIt && i[curdex-1] >= r) {
^
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rhdf5lib/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c numeric_matrix.cpp -o numeric_matrix.o
In file included from Input_matrix.h:11:0,
from LIN_matrix.h:4,
from numeric_matrix.h:4,
from numeric_matrix.cpp:1:
Psymm_matrix.h: In instantiation of 'beachmat::Psymm_matrix<T, V>::Psymm_matrix(const RObject&) [with T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]':
LIN_methods.h:116:96: required from 'beachmat::advanced_lin_matrix<T, V, M>::advanced_lin_matrix(const RObject&) [with T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; M = beachmat::Psymm_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]'
numeric_matrix.cpp:39:85: required from here
Psymm_matrix.h:55:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (x.size()!=(NR*(NR+1))/2) { throw_custom_error("length of 'x' in a ", ctype, " object is inconsistent with its dimensions"); }
^
In file included from Input_matrix.h:9:0,
from LIN_matrix.h:4,
from numeric_matrix.h:4,
from numeric_matrix.cpp:1:
dense_matrix.h: In instantiation of 'beachmat::dense_matrix<T, V>::dense_matrix(const RObject&) [with T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]':
LIN_methods.h:116:96: required from 'beachmat::advanced_lin_matrix<T, V, M>::advanced_lin_matrix(const RObject&) [with T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; M = beachmat::dense_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]'
LIN_methods.h:194:118: required from 'beachmat::dense_lin_matrix<T, V>::dense_lin_matrix(const RObject&) [with T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]'
numeric_matrix.cpp:33:85: required from here
dense_matrix.h:50:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (x.size()!=(this->nrow)*NC) {
^
In file included from Input_matrix.h:10:0,
from LIN_matrix.h:4,
from numeric_matrix.h:4,
from numeric_matrix.cpp:1:
Csparse_matrix.h: In instantiation of 'beachmat::Csparse_matrix<T, V>::Csparse_matrix(const RObject&) [with T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]':
LIN_methods.h:116:96: required from 'beachmat::advanced_lin_matrix<T, V, M>::advanced_lin_matrix(const RObject&) [with T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; M = beachmat::Csparse_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]'
LIN_methods.h:212:124: required from 'beachmat::Csparse_lin_matrix<T, V>::Csparse_lin_matrix(const RObject&) [with T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]'
numeric_matrix.cpp:35:87: required from here
Csparse_matrix.h:72:13: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (NC+1!=p.size()) { throw_custom_error("length of 'p' slot in a ", ctype, " object should be equal to 'ncol+1'"); }
^
Csparse_matrix.h:101:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (curi<0 || curi>=NR) {
^
In file included from Input_matrix.h:8:0,
from LIN_matrix.h:4,
from numeric_matrix.h:4,
from numeric_matrix.cpp:1:
simple_matrix.h: In instantiation of 'beachmat::simple_matrix<T, V>::simple_matrix(const RObject&) [with T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]':
LIN_methods.h:116:96: required from 'beachmat::advanced_lin_matrix<T, V, M>::advanced_lin_matrix(const RObject&) [with T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; M = beachmat::simple_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]'
LIN_methods.h:178:121: required from 'beachmat::simple_lin_matrix<T, V>::simple_lin_matrix(const RObject&) [with T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]'
numeric_matrix.cpp:53:78: required from here
simple_matrix.h:49:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (mat.size()!=(this->nrow)*NC) {
^
In file included from Input_matrix.h:10:0,
from LIN_matrix.h:4,
from numeric_matrix.h:4,
from numeric_matrix.cpp:1:
Csparse_matrix.h: In instantiation of 'void beachmat::Csparse_matrix<T, V>::get_row(size_t, Iter, size_t, size_t) [with Iter = int*; T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; size_t = long long unsigned int]':
LIN_methods.h:145:5: required from 'void beachmat::advanced_lin_matrix<T, V, M>::get_row(size_t, Rcpp::Vector<13>::iterator, size_t, size_t) [with T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; M = beachmat::Csparse_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >; size_t = long long unsigned int; Rcpp::Vector<13>::iterator = int*; Rcpp::traits::storage_type<13>::type = int]'
numeric_matrix.cpp:72:1: required from here
Csparse_matrix.h:199:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (idex!=*pIt && i[idex]==r) { (*out)=x[idex]; }
^
Csparse_matrix.h: In instantiation of 'void beachmat::Csparse_matrix<T, V>::get_row(size_t, Iter, size_t, size_t) [with Iter = double*; T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; size_t = long long unsigned int]':
LIN_methods.h:151:5: required from 'void beachmat::advanced_lin_matrix<T, V, M>::get_row(size_t, Rcpp::Vector<14, Rcpp::PreserveStorage>::iterator, size_t, size_t) [with T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; M = beachmat::Csparse_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >; size_t = long long unsigned int; Rcpp::Vector<14, Rcpp::PreserveStorage>::iterator = double*; Rcpp::traits::storage_type<14>::type = double]'
numeric_matrix.cpp:72:1: required from here
Csparse_matrix.h:199:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Csparse_matrix.h: In instantiation of 'T beachmat::Csparse_matrix<T, V>::get(size_t, size_t) [with T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; size_t = long long unsigned int]':
LIN_methods.h:157:24: required from 'T beachmat::advanced_lin_matrix<T, V, M>::get(size_t, size_t) [with T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; M = beachmat::Csparse_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >; size_t = long long unsigned int]'
numeric_matrix.cpp:72:1: required from here
Csparse_matrix.h:119:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (loc!=iend && *loc==r) {
^
Csparse_matrix.h: In instantiation of 'size_t beachmat::Csparse_matrix<T, V>::get_nonzero_row(size_t, Rcpp::Vector<13>::iterator, Iter, size_t, size_t) [with Iter = int*; T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; size_t = long long unsigned int; Rcpp::Vector<13>::iterator = int*; Rcpp::traits::storage_type<13>::type = int]':
LIN_methods.h:229:62: required from 'size_t beachmat::Csparse_lin_matrix<T, V>::get_nonzero_row(size_t, Rcpp::Vector<13>::iterator, Rcpp::Vector<13>::iterator, size_t, size_t) [with T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; size_t = long long unsigned int; Rcpp::Vector<13>::iterator = int*; Rcpp::traits::storage_type<13>::type = int]'
numeric_matrix.cpp:72:1: required from here
Csparse_matrix.h:239:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (idex!=*pIt && i[idex]==r) {
^
Csparse_matrix.h: In instantiation of 'size_t beachmat::Csparse_matrix<T, V>::get_nonzero_row(size_t, Rcpp::Vector<13>::iterator, Iter, size_t, size_t) [with Iter = double*; T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; size_t = long long unsigned int; Rcpp::Vector<13>::iterator = int*; Rcpp::traits::storage_type<13>::type = int]':
LIN_methods.h:234:62: required from 'size_t beachmat::Csparse_lin_matrix<T, V>::get_nonzero_row(size_t, Rcpp::Vector<13>::iterator, Rcpp::Vector<14, Rcpp::PreserveStorage>::iterator, size_t, size_t) [with T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; size_t = long long unsigned int; Rcpp::Vector<13>::iterator = int*; Rcpp::traits::storage_type<13>::type = int; Rcpp::Vector<14, Rcpp::PreserveStorage>::iterator = double*; Rcpp::traits::storage_type<14>::type = double]'
numeric_matrix.cpp:72:1: required from here
Csparse_matrix.h:239:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Csparse_matrix.h: In instantiation of 'void beachmat::Csparse_matrix<T, V>::update_indices(size_t, size_t, size_t) [with T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; size_t = long long unsigned int]':
Csparse_matrix.h:193:34: required from 'void beachmat::Csparse_matrix<T, V>::get_row(size_t, Iter, size_t, size_t) [with Iter = int*; T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; size_t = long long unsigned int]'
LIN_methods.h:145:5: required from 'void beachmat::advanced_lin_matrix<T, V, M>::get_row(size_t, Rcpp::Vector<13>::iterator, size_t, size_t) [with T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; M = beachmat::Csparse_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >; size_t = long long unsigned int; Rcpp::Vector<13>::iterator = int*; Rcpp::traits::storage_type<13>::type = int]'
numeric_matrix.cpp:72:1: required from here
Csparse_matrix.h:155:43: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (curdex!=*pIt && i[curdex] < r) {
^
Csparse_matrix.h:162:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (curdex!=*pIt && i[curdex-1] >= r) {
^
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rhdf5lib/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c output_param.cpp -o output_param.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rhdf5lib/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c repacker.cpp -o repacker.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rhdf5lib/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c utils.cpp -o utils.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o beachmat.dll tmp.def HDF5_utils.o any_matrix.o character_matrix.o character_output.o find_chunks.o functions.o integer_matrix.o logical_matrix.o numeric_matrix.o output_param.o repacker.o utils.o -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/library/Rhdf5lib/lib/x64 -lhdf5_cpp -lhdf5 -lszip -lz -lpsapi -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/x64 -lR -lm -LC:/local323/lib/x64 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/x64 -lR
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o libbeachmat.dll any_matrix.o character_matrix.o character_output.o integer_matrix.o logical_matrix.o numeric_matrix.o utils.o HDF5_utils.o output_param.o -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/library/Rhdf5lib/lib/x64 -lhdf5_cpp -lhdf5 -lszip -lz -lpsapi -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/x64 -lR -lm
C:/Rtools/mingw_64/bin/ar crs libbeachmat.a any_matrix.o character_matrix.o character_output.o integer_matrix.o logical_matrix.o numeric_matrix.o utils.o HDF5_utils.o output_param.o
mkdir -p "C:/Users/biocbuild/bbs-3.6-bioc/meat/beachmat.buildbin-libdir/beachmat/lib/x64" "C:/Users/biocbuild/bbs-3.6-bioc/meat/beachmat.buildbin-libdir/beachmat/include/beachmat"
cp any_matrix.h utils.h beachmat.h HDF5_utils.h output_param.h Psymm_matrix.h HDF5_matrix.h Csparse_matrix.h dense_matrix.h simple_matrix.h Rle_matrix.h Input_matrix.h simple_output.h Csparse_output.h HDF5_output.h Output_matrix.h LIN_matrix.h LIN_methods.h LIN_output.h LIN_outfun.h logical_matrix.h integer_matrix.h character_matrix.h numeric_matrix.h character_output.h "C:/Users/biocbuild/bbs-3.6-bioc/meat/beachmat.buildbin-libdir/beachmat/include/beachmat"
mv libbeachmat.* "C:/Users/biocbuild/bbs-3.6-bioc/meat/beachmat.buildbin-libdir/beachmat/lib/x64"
installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/beachmat.buildbin-libdir/beachmat/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'beachmat' as beachmat_1.0.2.zip
* DONE (beachmat)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.6-bioc/R/library'
package 'beachmat' successfully unpacked and MD5 sums checked
In R CMD INSTALL
