Package: beachmat

Version: 1.2.1

Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:beachmat.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings beachmat_1.2.1.tar.gz

StartedAt: 2018-10-17 00:39:10 -0400 (Wed, 17 Oct 2018)

EndedAt: 2018-10-17 00:55:43 -0400 (Wed, 17 Oct 2018)

EllapsedTime: 993.5 seconds

RetCode: 0

Status:  OK

CheckDir: beachmat.Rcheck

Warnings: 0

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:beachmat.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings beachmat_1.2.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/beachmat.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'beachmat/DESCRIPTION' ... OK
* this is package 'beachmat' version '1.2.1'
* package encoding: UTF-8
* 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 'beachmat' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 23.9Mb
  sub-directories of 1Mb or more:
    lib   14.2Mb
    libs   9.3Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII 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 cross-references ... 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 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/bbs-3.7-bioc/R/library/beachmat/libs/i386/beachmat.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' ... OK
** running examples for arch 'x64' ... OK
* 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 re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.7-bioc/meat/beachmat.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/beachmat_1.2.1.tar.gz && rm -rf beachmat.buildbin-libdir && mkdir beachmat.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=beachmat.buildbin-libdir beachmat_1.2.1.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL beachmat_1.2.1.zip && rm beachmat_1.2.1.tar.gz beachmat_1.2.1.zip
###
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100 68395  100 68395    0     0  1234k      0 --:--:-- --:--:-- --:--:-- 1421k

install for i386

* installing *source* package 'beachmat' ...
** libs
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include"   -I"C:/extsoft/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˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include"   -I"C:/extsoft/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˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c character_matrix.cpp -o character_matrix.o
character_matrix.cpp: In member function 'virtual beachmat::const_col_indexed_info<Rcpp::Vector<16> > beachmat::character_matrix::get_const_col_indexed(size_t, Rcpp::Vector<16>::iterator, size_t, size_t)':
character_matrix.cpp:33:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (indices.size()!=this->get_nrow()) {
                       ^
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.h:46:75:   required from 'beachmat::general_character_matrix<M>::general_character_matrix(const RObject&) [with M = beachmat::simple_matrix<Rcpp::String, Rcpp::Vector<16> >; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]'
character_matrix.cpp:42:119:   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 delayed_matrix.h:109:0,
                 from Input_matrix.h:14,
                 from character_matrix.h:4,
                 from character_matrix.cpp:1:
delayed_methods.h: In instantiation of 'static void beachmat::delayed_coord_transformer<T, V>::obtain_indices(const RObject&, size_t, bool&, size_t&, std::vector<unsigned int>&) [with T = Rcpp::String; V = Rcpp::Vector<16>; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>; size_t = unsigned int]':
delayed_methods.h:27:80:   required from 'beachmat::delayed_coord_transformer<T, V>::delayed_coord_transformer(const List&, const LogicalVector&, M) [with M = beachmat::character_matrix*; T = Rcpp::String; V = Rcpp::Vector<16>; Rcpp::List = Rcpp::Vector<19>; Rcpp::LogicalVector = Rcpp::Vector<10, Rcpp::PreserveStorage>]'
delayed_methods.h:269:20:   required from 'beachmat::delayed_matrix<T, V, base_mat>::delayed_matrix(const RObject&) [with T = Rcpp::String; V = Rcpp::Vector<16>; base_mat = beachmat::character_matrix; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]'
character_matrix.h:46:75:   required from 'beachmat::general_character_matrix<M>::general_character_matrix(const RObject&) [with M = beachmat::delayed_matrix<Rcpp::String, Rcpp::Vector<16>, beachmat::character_matrix>; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]'
character_matrix.cpp:113:91:   required from here
delayed_methods.h:66:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (i < 1 || i > original_dim) {
                        ^
In file included from delayed_methods.h:2:0,
                 from delayed_matrix.h:109,
                 from Input_matrix.h:14,
                 from character_matrix.h:4,
                 from character_matrix.cpp:1:
unknown_matrix.h: In instantiation of 'void beachmat::unknown_matrix<T, V>::update_storage_by_row(size_t) [with T = Rcpp::String; V = Rcpp::Vector<16>; size_t = unsigned int]':
unknown_matrix.h:92:28:   required from 'void beachmat::unknown_matrix<T, V>::get_row(size_t, Iter, size_t, size_t) [with Iter = Rcpp::internal::Proxy_Iterator<Rcpp::internal::string_proxy<16> >; T = Rcpp::String; V = Rcpp::Vector<16>; size_t = unsigned int]'
character_matrix.h:52:129:   required from 'void beachmat::general_character_matrix<M>::get_row(size_t, Rcpp::Vector<16>::iterator, size_t, size_t) [with M = beachmat::unknown_matrix<Rcpp::String, Rcpp::Vector<16> >; size_t = unsigned int; Rcpp::Vector<16>::iterator = Rcpp::internal::Proxy_Iterator<Rcpp::internal::string_proxy<16> >]'
character_matrix.cpp:125:1:   required from here
unknown_matrix.h:65:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (r < row_indices[0] || r >= row_indices[1]) {
                                 ^
unknown_matrix.h:65:11: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (r < row_indices[0] || r >= row_indices[1]) {
           ^
unknown_matrix.h: In instantiation of 'void beachmat::unknown_matrix<T, V>::update_storage_by_col(size_t) [with T = Rcpp::String; V = Rcpp::Vector<16>; size_t = unsigned int]':
unknown_matrix.h:102:28:   required from 'void beachmat::unknown_matrix<T, V>::get_col(size_t, Iter, size_t, size_t) [with Iter = Rcpp::internal::Proxy_Iterator<Rcpp::internal::string_proxy<16> >; T = Rcpp::String; V = Rcpp::Vector<16>; size_t = unsigned int]'
character_matrix.h:53:129:   required from 'void beachmat::general_character_matrix<M>::get_col(size_t, Rcpp::Vector<16>::iterator, size_t, size_t) [with M = beachmat::unknown_matrix<Rcpp::String, Rcpp::Vector<16> >; size_t = unsigned int; Rcpp::Vector<16>::iterator = Rcpp::internal::Proxy_Iterator<Rcpp::internal::string_proxy<16> >]'
character_matrix.cpp:125:1:   required from here
unknown_matrix.h:74:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (c < col_indices[0] || c >= col_indices[1]) {
                                 ^
unknown_matrix.h:74:11: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (c < col_indices[0] || c >= col_indices[1]) {
           ^
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include"   -I"C:/extsoft/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˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include"   -I"C:/extsoft/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˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include"   -I"C:/extsoft/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˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include"   -I"C:/extsoft/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:68:94:   required from 'beachmat::general_lin_matrix<T, V, M>::general_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:130:100:   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:49:78:   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 delayed_matrix.h:109:0,
                 from Input_matrix.h:14,
                 from LIN_matrix.h:4,
                 from integer_matrix.h:4,
                 from integer_matrix.cpp:1:
delayed_methods.h: In instantiation of 'static void beachmat::delayed_coord_transformer<T, V>::obtain_indices(const RObject&, size_t, bool&, size_t&, std::vector<unsigned int>&) [with T = int; V = Rcpp::Vector<13>; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>; size_t = unsigned int]':
delayed_methods.h:27:80:   required from 'beachmat::delayed_coord_transformer<T, V>::delayed_coord_transformer(const List&, const LogicalVector&, M) [with M = beachmat::lin_matrix<int, Rcpp::Vector<13> >*; T = int; V = Rcpp::Vector<13>; Rcpp::List = Rcpp::Vector<19>; Rcpp::LogicalVector = Rcpp::Vector<10, Rcpp::PreserveStorage>]'
delayed_methods.h:269:20:   required from 'beachmat::delayed_matrix<T, V, base_mat>::delayed_matrix(const RObject&) [with T = int; V = Rcpp::Vector<13>; base_mat = beachmat::lin_matrix<int, Rcpp::Vector<13> >; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]'
LIN_methods.h:68:94:   required from 'beachmat::general_lin_matrix<T, V, M>::general_lin_matrix(const RObject&) [with T = int; V = Rcpp::Vector<13>; M = beachmat::delayed_matrix<int, Rcpp::Vector<13>, beachmat::lin_matrix<int, Rcpp::Vector<13> > >; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]'
integer_matrix.cpp:45:87:   required from here
delayed_methods.h:66:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (i < 1 || i > original_dim) {
                        ^
In file included from LIN_matrix.h:174:0,
                 from integer_matrix.h:4,
                 from integer_matrix.cpp:1:
LIN_methods.h: In instantiation of 'beachmat::const_col_indexed_info<V> beachmat::lin_matrix<T, V>::get_const_col_indexed(size_t, typename V::iterator, size_t, size_t) [with T = int; V = Rcpp::Vector<13>; beachmat::const_col_indexed_info<V> = std::tuple<unsigned int, int*, int*>; typename V::iterator = int*; size_t = unsigned int; typename V::iterator = int*]':
integer_matrix.cpp:70:1:   required from here
LIN_methods.h:58:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (indices.size()!=this->get_nrow()) {
                       ^
In file included from delayed_methods.h:2:0,
                 from delayed_matrix.h:109,
                 from Input_matrix.h:14,
                 from LIN_matrix.h:4,
                 from integer_matrix.h:4,
                 from integer_matrix.cpp:1:
unknown_matrix.h: In instantiation of 'void beachmat::unknown_matrix<T, V>::update_storage_by_row(size_t) [with T = int; V = Rcpp::Vector<13>; size_t = unsigned int]':
unknown_matrix.h:92:28:   required from 'void beachmat::unknown_matrix<T, V>::get_row(size_t, Iter, size_t, size_t) [with Iter = int*; T = int; V = Rcpp::Vector<13>; size_t = unsigned int]'
LIN_methods.h:97:5:   required from 'void beachmat::general_lin_matrix<T, V, M>::get_row(size_t, Rcpp::Vector<13>::iterator, size_t, size_t) [with T = int; V = Rcpp::Vector<13>; M = beachmat::unknown_matrix<int, Rcpp::Vector<13> >; size_t = unsigned int; Rcpp::Vector<13>::iterator = int*; Rcpp::traits::storage_type<13>::type = int]'
integer_matrix.cpp:70:1:   required from here
unknown_matrix.h:65:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (r < row_indices[0] || r >= row_indices[1]) {
                                 ^
unknown_matrix.h:65:11: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (r < row_indices[0] || r >= row_indices[1]) {
           ^
unknown_matrix.h: In instantiation of 'void beachmat::unknown_matrix<T, V>::update_storage_by_col(size_t) [with T = int; V = Rcpp::Vector<13>; size_t = unsigned int]':
unknown_matrix.h:102:28:   required from 'void beachmat::unknown_matrix<T, V>::get_col(size_t, Iter, size_t, size_t) [with Iter = int*; T = int; V = Rcpp::Vector<13>; size_t = unsigned int]'
LIN_methods.h:85:5:   required from 'void beachmat::general_lin_matrix<T, V, M>::get_col(size_t, Rcpp::Vector<13>::iterator, size_t, size_t) [with T = int; V = Rcpp::Vector<13>; M = beachmat::unknown_matrix<int, Rcpp::Vector<13> >; size_t = unsigned int; Rcpp::Vector<13>::iterator = int*; Rcpp::traits::storage_type<13>::type = int]'
integer_matrix.cpp:70:1:   required from here
unknown_matrix.h:74:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (c < col_indices[0] || c >= col_indices[1]) {
                                 ^
unknown_matrix.h:74:11: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (c < col_indices[0] || c >= col_indices[1]) {
           ^
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include"   -I"C:/extsoft/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:68:94:   required from 'beachmat::general_lin_matrix<T, V, M>::general_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:57:85:   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:68:94:   required from 'beachmat::general_lin_matrix<T, V, M>::general_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:148:97:   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:51:85:   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:68:94:   required from 'beachmat::general_lin_matrix<T, V, M>::general_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:166:103:   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:53:87:   required from here
Csparse_matrix.h:68:13: 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:96:27: 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:68:94:   required from 'beachmat::general_lin_matrix<T, V, M>::general_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:130:100:   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:67:78:   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 delayed_matrix.h:109:0,
                 from Input_matrix.h:14,
                 from LIN_matrix.h:4,
                 from logical_matrix.h:4,
                 from logical_matrix.cpp:1:
delayed_methods.h: In instantiation of 'static void beachmat::delayed_coord_transformer<T, V>::obtain_indices(const RObject&, size_t, bool&, size_t&, std::vector<unsigned int>&) [with T = int; V = Rcpp::Vector<10, Rcpp::PreserveStorage>; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>; size_t = unsigned int]':
delayed_methods.h:27:80:   required from 'beachmat::delayed_coord_transformer<T, V>::delayed_coord_transformer(const List&, const LogicalVector&, M) [with M = beachmat::lin_matrix<int, Rcpp::Vector<10, Rcpp::PreserveStorage> >*; T = int; V = Rcpp::Vector<10, Rcpp::PreserveStorage>; Rcpp::List = Rcpp::Vector<19>; Rcpp::LogicalVector = Rcpp::Vector<10, Rcpp::PreserveStorage>]'
delayed_methods.h:269:20:   required from 'beachmat::delayed_matrix<T, V, base_mat>::delayed_matrix(const RObject&) [with T = int; V = Rcpp::Vector<10, Rcpp::PreserveStorage>; base_mat = beachmat::lin_matrix<int, Rcpp::Vector<10, Rcpp::PreserveStorage> >; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]'
LIN_methods.h:68:94:   required from 'beachmat::general_lin_matrix<T, V, M>::general_lin_matrix(const RObject&) [with T = int; V = Rcpp::Vector<10, Rcpp::PreserveStorage>; M = beachmat::delayed_matrix<int, Rcpp::Vector<10, Rcpp::PreserveStorage>, beachmat::lin_matrix<int, Rcpp::Vector<10, Rcpp::PreserveStorage> > >; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]'
logical_matrix.cpp:63:87:   required from here
delayed_methods.h:66:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (i < 1 || i > original_dim) {
                        ^
In file included from LIN_matrix.h:174:0,
                 from logical_matrix.h:4,
                 from logical_matrix.cpp:1:
LIN_methods.h: In instantiation of 'beachmat::const_col_indexed_info<V> beachmat::lin_matrix<T, V>::get_const_col_indexed(size_t, typename V::iterator, size_t, size_t) [with T = int; V = Rcpp::Vector<10, Rcpp::PreserveStorage>; beachmat::const_col_indexed_info<V> = std::tuple<unsigned int, int*, int*>; typename V::iterator = int*; size_t = unsigned int; typename V::iterator = int*]':
logical_matrix.cpp:90:1:   required from here
LIN_methods.h:58:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (indices.size()!=this->get_nrow()) {
                       ^
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:97:5:   required from 'void beachmat::general_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:90:1:   required from here
Csparse_matrix.h:201:34: 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:103:5:   required from 'void beachmat::general_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:90:1:   required from here
Csparse_matrix.h:201:34: 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:109:24:   required from 'T beachmat::general_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:90:1:   required from here
Csparse_matrix.h:114:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (loc!=iend && *loc==r) { 
                          ^
In file included from delayed_methods.h:2:0,
                 from delayed_matrix.h:109,
                 from Input_matrix.h:14,
                 from LIN_matrix.h:4,
                 from logical_matrix.h:4,
                 from logical_matrix.cpp:1:
unknown_matrix.h: In instantiation of 'void beachmat::unknown_matrix<T, V>::update_storage_by_row(size_t) [with T = int; V = Rcpp::Vector<10, Rcpp::PreserveStorage>; size_t = unsigned int]':
unknown_matrix.h:92:28:   required from 'void beachmat::unknown_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:97:5:   required from 'void beachmat::general_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::unknown_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:90:1:   required from here
unknown_matrix.h:65:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (r < row_indices[0] || r >= row_indices[1]) {
                                 ^
unknown_matrix.h:65:11: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (r < row_indices[0] || r >= row_indices[1]) {
           ^
unknown_matrix.h: In instantiation of 'void beachmat::unknown_matrix<T, V>::update_storage_by_col(size_t) [with T = int; V = Rcpp::Vector<10, Rcpp::PreserveStorage>; size_t = unsigned int]':
unknown_matrix.h:102:28:   required from 'void beachmat::unknown_matrix<T, V>::get_col(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:85:5:   required from 'void beachmat::general_lin_matrix<T, V, M>::get_col(size_t, Rcpp::Vector<13>::iterator, size_t, size_t) [with T = int; V = Rcpp::Vector<10, Rcpp::PreserveStorage>; M = beachmat::unknown_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:90:1:   required from here
unknown_matrix.h:74:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (c < col_indices[0] || c >= col_indices[1]) {
                                 ^
unknown_matrix.h:74:11: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (c < col_indices[0] || c >= col_indices[1]) {
           ^
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>::update_indices(size_t, size_t, size_t) [with T = int; V = Rcpp::Vector<10, Rcpp::PreserveStorage>; size_t = unsigned int]':
Csparse_matrix.h:195:34:   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:97:5:   required from 'void beachmat::general_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:90:1:   required from here
Csparse_matrix.h:157:43: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             if (curdex!=*pIt && i[curdex] < r) { 
                                           ^
Csparse_matrix.h:164:45: 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˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include"   -I"C:/extsoft/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:68:94:   required from 'beachmat::general_lin_matrix<T, V, M>::general_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:57:85:   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:68:94:   required from 'beachmat::general_lin_matrix<T, V, M>::general_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:148:97:   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:51:85:   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:68:94:   required from 'beachmat::general_lin_matrix<T, V, M>::general_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:166:103:   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:53:87:   required from here
Csparse_matrix.h:68:13: 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:96:27: 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:68:94:   required from 'beachmat::general_lin_matrix<T, V, M>::general_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:130:100:   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:67:78:   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 delayed_matrix.h:109:0,
                 from Input_matrix.h:14,
                 from LIN_matrix.h:4,
                 from numeric_matrix.h:4,
                 from numeric_matrix.cpp:1:
delayed_methods.h: In instantiation of 'static void beachmat::delayed_coord_transformer<T, V>::obtain_indices(const RObject&, size_t, bool&, size_t&, std::vector<unsigned int>&) [with T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>; size_t = unsigned int]':
delayed_methods.h:27:80:   required from 'beachmat::delayed_coord_transformer<T, V>::delayed_coord_transformer(const List&, const LogicalVector&, M) [with M = beachmat::lin_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >*; T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; Rcpp::List = Rcpp::Vector<19>; Rcpp::LogicalVector = Rcpp::Vector<10, Rcpp::PreserveStorage>]'
delayed_methods.h:269:20:   required from 'beachmat::delayed_matrix<T, V, base_mat>::delayed_matrix(const RObject&) [with T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; base_mat = beachmat::lin_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]'
LIN_methods.h:68:94:   required from 'beachmat::general_lin_matrix<T, V, M>::general_lin_matrix(const RObject&) [with T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; M = beachmat::delayed_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage>, beachmat::lin_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> > >; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]'
numeric_matrix.cpp:63:87:   required from here
delayed_methods.h:66:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (i < 1 || i > original_dim) {
                        ^
In file included from LIN_matrix.h:174:0,
                 from numeric_matrix.h:4,
                 from numeric_matrix.cpp:1:
LIN_methods.h: In instantiation of 'beachmat::const_col_indexed_info<V> beachmat::lin_matrix<T, V>::get_const_col_indexed(size_t, typename V::iterator, size_t, size_t) [with T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; beachmat::const_col_indexed_info<V> = std::tuple<unsigned int, int*, double*>; typename V::iterator = double*; size_t = unsigned int; typename V::iterator = double*]':
numeric_matrix.cpp:90:1:   required from here
LIN_methods.h:58:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (indices.size()!=this->get_nrow()) {
                       ^
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:97:5:   required from 'void beachmat::general_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:90:1:   required from here
Csparse_matrix.h:201:34: 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:103:5:   required from 'void beachmat::general_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:90:1:   required from here
Csparse_matrix.h:201:34: 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:109:24:   required from 'T beachmat::general_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:90:1:   required from here
Csparse_matrix.h:114:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (loc!=iend && *loc==r) { 
                          ^
In file included from delayed_methods.h:2:0,
                 from delayed_matrix.h:109,
                 from Input_matrix.h:14,
                 from LIN_matrix.h:4,
                 from numeric_matrix.h:4,
                 from numeric_matrix.cpp:1:
unknown_matrix.h: In instantiation of 'void beachmat::unknown_matrix<T, V>::update_storage_by_row(size_t) [with T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; size_t = unsigned int]':
unknown_matrix.h:92:28:   required from 'void beachmat::unknown_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:97:5:   required from 'void beachmat::general_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::unknown_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:90:1:   required from here
unknown_matrix.h:65:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (r < row_indices[0] || r >= row_indices[1]) {
                                 ^
unknown_matrix.h:65:11: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (r < row_indices[0] || r >= row_indices[1]) {
           ^
unknown_matrix.h: In instantiation of 'void beachmat::unknown_matrix<T, V>::update_storage_by_col(size_t) [with T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; size_t = unsigned int]':
unknown_matrix.h:102:28:   required from 'void beachmat::unknown_matrix<T, V>::get_col(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:85:5:   required from 'void beachmat::general_lin_matrix<T, V, M>::get_col(size_t, Rcpp::Vector<13>::iterator, size_t, size_t) [with T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; M = beachmat::unknown_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:90:1:   required from here
unknown_matrix.h:74:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (c < col_indices[0] || c >= col_indices[1]) {
                                 ^
unknown_matrix.h:74:11: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (c < col_indices[0] || c >= col_indices[1]) {
           ^
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>::update_indices(size_t, size_t, size_t) [with T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; size_t = unsigned int]':
Csparse_matrix.h:195:34:   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:97:5:   required from 'void beachmat::general_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:90:1:   required from here
Csparse_matrix.h:157:43: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             if (curdex!=*pIt && i[curdex] < r) { 
                                           ^
Csparse_matrix.h:164:45: 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˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include"   -I"C:/extsoft/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˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include"   -I"C:/extsoft/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˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include"   -I"C:/extsoft/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˜1.7-B/R/library/Rhdf5lib/lib/i386 -lhdf5_cpp -lhdf5 -lszip -lz -lpsapi -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/i386 -lR -lm -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.7-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˜1.7-B/R/library/Rhdf5lib/lib/i386 -lhdf5_cpp -lhdf5 -lszip -lz -lpsapi   -LC:/Users/BIOCBU˜1/BBS-3˜1.7-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-3.7-bioc/meat/beachmat.buildbin-libdir/beachmat/lib/i386" "C:/Users/biocbuild/bbs-3.7-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 delayed_matrix.h delayed_methods.h unknown_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-3.7-bioc/meat/beachmat.buildbin-libdir/beachmat/include/beachmat"
mv libbeachmat.* "C:/Users/biocbuild/bbs-3.7-bioc/meat/beachmat.buildbin-libdir/beachmat/lib/i386"
installing to C:/Users/biocbuild/bbs-3.7-bioc/meat/beachmat.buildbin-libdir/beachmat/libs/i386
** R
** inst
** byte-compile and prepare 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˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include"   -I"C:/extsoft/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˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include"   -I"C:/extsoft/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˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c character_matrix.cpp -o character_matrix.o
character_matrix.cpp: In member function 'virtual beachmat::const_col_indexed_info<Rcpp::Vector<16> > beachmat::character_matrix::get_const_col_indexed(size_t, Rcpp::Vector<16>::iterator, size_t, size_t)':
character_matrix.cpp:33:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (indices.size()!=this->get_nrow()) {
                       ^
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.h:46:75:   required from 'beachmat::general_character_matrix<M>::general_character_matrix(const RObject&) [with M = beachmat::simple_matrix<Rcpp::String, Rcpp::Vector<16> >; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]'
character_matrix.cpp:42:119:   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 delayed_matrix.h:109:0,
                 from Input_matrix.h:14,
                 from character_matrix.h:4,
                 from character_matrix.cpp:1:
delayed_methods.h: In instantiation of 'static void beachmat::delayed_coord_transformer<T, V>::obtain_indices(const RObject&, size_t, bool&, size_t&, std::vector<long long unsigned int>&) [with T = Rcpp::String; V = Rcpp::Vector<16>; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>; size_t = long long unsigned int]':
delayed_methods.h:27:80:   required from 'beachmat::delayed_coord_transformer<T, V>::delayed_coord_transformer(const List&, const LogicalVector&, M) [with M = beachmat::character_matrix*; T = Rcpp::String; V = Rcpp::Vector<16>; Rcpp::List = Rcpp::Vector<19>; Rcpp::LogicalVector = Rcpp::Vector<10, Rcpp::PreserveStorage>]'
delayed_methods.h:269:20:   required from 'beachmat::delayed_matrix<T, V, base_mat>::delayed_matrix(const RObject&) [with T = Rcpp::String; V = Rcpp::Vector<16>; base_mat = beachmat::character_matrix; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]'
character_matrix.h:46:75:   required from 'beachmat::general_character_matrix<M>::general_character_matrix(const RObject&) [with M = beachmat::delayed_matrix<Rcpp::String, Rcpp::Vector<16>, beachmat::character_matrix>; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]'
character_matrix.cpp:113:91:   required from here
delayed_methods.h:66:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (i < 1 || i > original_dim) {
                        ^
In file included from delayed_methods.h:2:0,
                 from delayed_matrix.h:109,
                 from Input_matrix.h:14,
                 from character_matrix.h:4,
                 from character_matrix.cpp:1:
unknown_matrix.h: In instantiation of 'void beachmat::unknown_matrix<T, V>::update_storage_by_row(size_t) [with T = Rcpp::String; V = Rcpp::Vector<16>; size_t = long long unsigned int]':
unknown_matrix.h:92:28:   required from 'void beachmat::unknown_matrix<T, V>::get_row(size_t, Iter, size_t, size_t) [with Iter = Rcpp::internal::Proxy_Iterator<Rcpp::internal::string_proxy<16> >; T = Rcpp::String; V = Rcpp::Vector<16>; size_t = long long unsigned int]'
character_matrix.h:52:129:   required from 'void beachmat::general_character_matrix<M>::get_row(size_t, Rcpp::Vector<16>::iterator, size_t, size_t) [with M = beachmat::unknown_matrix<Rcpp::String, Rcpp::Vector<16> >; size_t = long long unsigned int; Rcpp::Vector<16>::iterator = Rcpp::internal::Proxy_Iterator<Rcpp::internal::string_proxy<16> >]'
character_matrix.cpp:125:1:   required from here
unknown_matrix.h:65:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (r < row_indices[0] || r >= row_indices[1]) {
                                 ^
unknown_matrix.h:65:11: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (r < row_indices[0] || r >= row_indices[1]) {
           ^
unknown_matrix.h: In instantiation of 'void beachmat::unknown_matrix<T, V>::update_storage_by_col(size_t) [with T = Rcpp::String; V = Rcpp::Vector<16>; size_t = long long unsigned int]':
unknown_matrix.h:102:28:   required from 'void beachmat::unknown_matrix<T, V>::get_col(size_t, Iter, size_t, size_t) [with Iter = Rcpp::internal::Proxy_Iterator<Rcpp::internal::string_proxy<16> >; T = Rcpp::String; V = Rcpp::Vector<16>; size_t = long long unsigned int]'
character_matrix.h:53:129:   required from 'void beachmat::general_character_matrix<M>::get_col(size_t, Rcpp::Vector<16>::iterator, size_t, size_t) [with M = beachmat::unknown_matrix<Rcpp::String, Rcpp::Vector<16> >; size_t = long long unsigned int; Rcpp::Vector<16>::iterator = Rcpp::internal::Proxy_Iterator<Rcpp::internal::string_proxy<16> >]'
character_matrix.cpp:125:1:   required from here
unknown_matrix.h:74:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (c < col_indices[0] || c >= col_indices[1]) {
                                 ^
unknown_matrix.h:74:11: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (c < col_indices[0] || c >= col_indices[1]) {
           ^
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include"   -I"C:/extsoft/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˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include"   -I"C:/extsoft/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˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include"   -I"C:/extsoft/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˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include"   -I"C:/extsoft/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:68:94:   required from 'beachmat::general_lin_matrix<T, V, M>::general_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:130:100:   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:49:78:   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 delayed_matrix.h:109:0,
                 from Input_matrix.h:14,
                 from LIN_matrix.h:4,
                 from integer_matrix.h:4,
                 from integer_matrix.cpp:1:
delayed_methods.h: In instantiation of 'static void beachmat::delayed_coord_transformer<T, V>::obtain_indices(const RObject&, size_t, bool&, size_t&, std::vector<long long unsigned int>&) [with T = int; V = Rcpp::Vector<13>; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>; size_t = long long unsigned int]':
delayed_methods.h:27:80:   required from 'beachmat::delayed_coord_transformer<T, V>::delayed_coord_transformer(const List&, const LogicalVector&, M) [with M = beachmat::lin_matrix<int, Rcpp::Vector<13> >*; T = int; V = Rcpp::Vector<13>; Rcpp::List = Rcpp::Vector<19>; Rcpp::LogicalVector = Rcpp::Vector<10, Rcpp::PreserveStorage>]'
delayed_methods.h:269:20:   required from 'beachmat::delayed_matrix<T, V, base_mat>::delayed_matrix(const RObject&) [with T = int; V = Rcpp::Vector<13>; base_mat = beachmat::lin_matrix<int, Rcpp::Vector<13> >; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]'
LIN_methods.h:68:94:   required from 'beachmat::general_lin_matrix<T, V, M>::general_lin_matrix(const RObject&) [with T = int; V = Rcpp::Vector<13>; M = beachmat::delayed_matrix<int, Rcpp::Vector<13>, beachmat::lin_matrix<int, Rcpp::Vector<13> > >; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]'
integer_matrix.cpp:45:87:   required from here
delayed_methods.h:66:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (i < 1 || i > original_dim) {
                        ^
In file included from LIN_matrix.h:174:0,
                 from integer_matrix.h:4,
                 from integer_matrix.cpp:1:
LIN_methods.h: In instantiation of 'beachmat::const_col_indexed_info<V> beachmat::lin_matrix<T, V>::get_const_col_indexed(size_t, typename V::iterator, size_t, size_t) [with T = int; V = Rcpp::Vector<13>; beachmat::const_col_indexed_info<V> = std::tuple<long long unsigned int, int*, int*>; typename V::iterator = int*; size_t = long long unsigned int; typename V::iterator = int*]':
integer_matrix.cpp:70:1:   required from here
LIN_methods.h:58:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (indices.size()!=this->get_nrow()) {
                       ^
In file included from delayed_methods.h:2:0,
                 from delayed_matrix.h:109,
                 from Input_matrix.h:14,
                 from LIN_matrix.h:4,
                 from integer_matrix.h:4,
                 from integer_matrix.cpp:1:
unknown_matrix.h: In instantiation of 'void beachmat::unknown_matrix<T, V>::update_storage_by_row(size_t) [with T = int; V = Rcpp::Vector<13>; size_t = long long unsigned int]':
unknown_matrix.h:92:28:   required from 'void beachmat::unknown_matrix<T, V>::get_row(size_t, Iter, size_t, size_t) [with Iter = int*; T = int; V = Rcpp::Vector<13>; size_t = long long unsigned int]'
LIN_methods.h:97:5:   required from 'void beachmat::general_lin_matrix<T, V, M>::get_row(size_t, Rcpp::Vector<13>::iterator, size_t, size_t) [with T = int; V = Rcpp::Vector<13>; M = beachmat::unknown_matrix<int, Rcpp::Vector<13> >; size_t = long long unsigned int; Rcpp::Vector<13>::iterator = int*; Rcpp::traits::storage_type<13>::type = int]'
integer_matrix.cpp:70:1:   required from here
unknown_matrix.h:65:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (r < row_indices[0] || r >= row_indices[1]) {
                                 ^
unknown_matrix.h:65:11: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (r < row_indices[0] || r >= row_indices[1]) {
           ^
unknown_matrix.h: In instantiation of 'void beachmat::unknown_matrix<T, V>::update_storage_by_col(size_t) [with T = int; V = Rcpp::Vector<13>; size_t = long long unsigned int]':
unknown_matrix.h:102:28:   required from 'void beachmat::unknown_matrix<T, V>::get_col(size_t, Iter, size_t, size_t) [with Iter = int*; T = int; V = Rcpp::Vector<13>; size_t = long long unsigned int]'
LIN_methods.h:85:5:   required from 'void beachmat::general_lin_matrix<T, V, M>::get_col(size_t, Rcpp::Vector<13>::iterator, size_t, size_t) [with T = int; V = Rcpp::Vector<13>; M = beachmat::unknown_matrix<int, Rcpp::Vector<13> >; size_t = long long unsigned int; Rcpp::Vector<13>::iterator = int*; Rcpp::traits::storage_type<13>::type = int]'
integer_matrix.cpp:70:1:   required from here
unknown_matrix.h:74:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (c < col_indices[0] || c >= col_indices[1]) {
                                 ^
unknown_matrix.h:74:11: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (c < col_indices[0] || c >= col_indices[1]) {
           ^
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include"   -I"C:/extsoft/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:68:94:   required from 'beachmat::general_lin_matrix<T, V, M>::general_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:57:85:   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:68:94:   required from 'beachmat::general_lin_matrix<T, V, M>::general_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:148:97:   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:51:85:   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:68:94:   required from 'beachmat::general_lin_matrix<T, V, M>::general_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:166:103:   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:53:87:   required from here
Csparse_matrix.h:68:13: 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:96:27: 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:68:94:   required from 'beachmat::general_lin_matrix<T, V, M>::general_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:130:100:   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:67:78:   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 delayed_matrix.h:109:0,
                 from Input_matrix.h:14,
                 from LIN_matrix.h:4,
                 from logical_matrix.h:4,
                 from logical_matrix.cpp:1:
delayed_methods.h: In instantiation of 'static void beachmat::delayed_coord_transformer<T, V>::obtain_indices(const RObject&, size_t, bool&, size_t&, std::vector<long long unsigned int>&) [with T = int; V = Rcpp::Vector<10, Rcpp::PreserveStorage>; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>; size_t = long long unsigned int]':
delayed_methods.h:27:80:   required from 'beachmat::delayed_coord_transformer<T, V>::delayed_coord_transformer(const List&, const LogicalVector&, M) [with M = beachmat::lin_matrix<int, Rcpp::Vector<10, Rcpp::PreserveStorage> >*; T = int; V = Rcpp::Vector<10, Rcpp::PreserveStorage>; Rcpp::List = Rcpp::Vector<19>; Rcpp::LogicalVector = Rcpp::Vector<10, Rcpp::PreserveStorage>]'
delayed_methods.h:269:20:   required from 'beachmat::delayed_matrix<T, V, base_mat>::delayed_matrix(const RObject&) [with T = int; V = Rcpp::Vector<10, Rcpp::PreserveStorage>; base_mat = beachmat::lin_matrix<int, Rcpp::Vector<10, Rcpp::PreserveStorage> >; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]'
LIN_methods.h:68:94:   required from 'beachmat::general_lin_matrix<T, V, M>::general_lin_matrix(const RObject&) [with T = int; V = Rcpp::Vector<10, Rcpp::PreserveStorage>; M = beachmat::delayed_matrix<int, Rcpp::Vector<10, Rcpp::PreserveStorage>, beachmat::lin_matrix<int, Rcpp::Vector<10, Rcpp::PreserveStorage> > >; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]'
logical_matrix.cpp:63:87:   required from here
delayed_methods.h:66:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (i < 1 || i > original_dim) {
                        ^
In file included from LIN_matrix.h:174:0,
                 from logical_matrix.h:4,
                 from logical_matrix.cpp:1:
LIN_methods.h: In instantiation of 'beachmat::const_col_indexed_info<V> beachmat::lin_matrix<T, V>::get_const_col_indexed(size_t, typename V::iterator, size_t, size_t) [with T = int; V = Rcpp::Vector<10, Rcpp::PreserveStorage>; beachmat::const_col_indexed_info<V> = std::tuple<long long unsigned int, int*, int*>; typename V::iterator = int*; size_t = long long unsigned int; typename V::iterator = int*]':
logical_matrix.cpp:90:1:   required from here
LIN_methods.h:58:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (indices.size()!=this->get_nrow()) {
                       ^
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:97:5:   required from 'void beachmat::general_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:90:1:   required from here
Csparse_matrix.h:201:34: 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:103:5:   required from 'void beachmat::general_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:90:1:   required from here
Csparse_matrix.h:201:34: 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:109:24:   required from 'T beachmat::general_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:90:1:   required from here
Csparse_matrix.h:114:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (loc!=iend && *loc==r) { 
                          ^
In file included from delayed_methods.h:2:0,
                 from delayed_matrix.h:109,
                 from Input_matrix.h:14,
                 from LIN_matrix.h:4,
                 from logical_matrix.h:4,
                 from logical_matrix.cpp:1:
unknown_matrix.h: In instantiation of 'void beachmat::unknown_matrix<T, V>::update_storage_by_row(size_t) [with T = int; V = Rcpp::Vector<10, Rcpp::PreserveStorage>; size_t = long long unsigned int]':
unknown_matrix.h:92:28:   required from 'void beachmat::unknown_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:97:5:   required from 'void beachmat::general_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::unknown_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:90:1:   required from here
unknown_matrix.h:65:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (r < row_indices[0] || r >= row_indices[1]) {
                                 ^
unknown_matrix.h:65:11: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (r < row_indices[0] || r >= row_indices[1]) {
           ^
unknown_matrix.h: In instantiation of 'void beachmat::unknown_matrix<T, V>::update_storage_by_col(size_t) [with T = int; V = Rcpp::Vector<10, Rcpp::PreserveStorage>; size_t = long long unsigned int]':
unknown_matrix.h:102:28:   required from 'void beachmat::unknown_matrix<T, V>::get_col(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:85:5:   required from 'void beachmat::general_lin_matrix<T, V, M>::get_col(size_t, Rcpp::Vector<13>::iterator, size_t, size_t) [with T = int; V = Rcpp::Vector<10, Rcpp::PreserveStorage>; M = beachmat::unknown_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:90:1:   required from here
unknown_matrix.h:74:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (c < col_indices[0] || c >= col_indices[1]) {
                                 ^
unknown_matrix.h:74:11: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (c < col_indices[0] || c >= col_indices[1]) {
           ^
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>::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:195:34:   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:97:5:   required from 'void beachmat::general_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:90:1:   required from here
Csparse_matrix.h:157:43: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             if (curdex!=*pIt && i[curdex] < r) { 
                                           ^
Csparse_matrix.h:164:45: 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˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include"   -I"C:/extsoft/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:68:94:   required from 'beachmat::general_lin_matrix<T, V, M>::general_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:57:85:   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:68:94:   required from 'beachmat::general_lin_matrix<T, V, M>::general_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:148:97:   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:51:85:   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:68:94:   required from 'beachmat::general_lin_matrix<T, V, M>::general_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:166:103:   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:53:87:   required from here
Csparse_matrix.h:68:13: 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:96:27: 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:68:94:   required from 'beachmat::general_lin_matrix<T, V, M>::general_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:130:100:   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:67:78:   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 delayed_matrix.h:109:0,
                 from Input_matrix.h:14,
                 from LIN_matrix.h:4,
                 from numeric_matrix.h:4,
                 from numeric_matrix.cpp:1:
delayed_methods.h: In instantiation of 'static void beachmat::delayed_coord_transformer<T, V>::obtain_indices(const RObject&, size_t, bool&, size_t&, std::vector<long long unsigned int>&) [with T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>; size_t = long long unsigned int]':
delayed_methods.h:27:80:   required from 'beachmat::delayed_coord_transformer<T, V>::delayed_coord_transformer(const List&, const LogicalVector&, M) [with M = beachmat::lin_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >*; T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; Rcpp::List = Rcpp::Vector<19>; Rcpp::LogicalVector = Rcpp::Vector<10, Rcpp::PreserveStorage>]'
delayed_methods.h:269:20:   required from 'beachmat::delayed_matrix<T, V, base_mat>::delayed_matrix(const RObject&) [with T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; base_mat = beachmat::lin_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]'
LIN_methods.h:68:94:   required from 'beachmat::general_lin_matrix<T, V, M>::general_lin_matrix(const RObject&) [with T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; M = beachmat::delayed_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage>, beachmat::lin_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> > >; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]'
numeric_matrix.cpp:63:87:   required from here
delayed_methods.h:66:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (i < 1 || i > original_dim) {
                        ^
In file included from LIN_matrix.h:174:0,
                 from numeric_matrix.h:4,
                 from numeric_matrix.cpp:1:
LIN_methods.h: In instantiation of 'beachmat::const_col_indexed_info<V> beachmat::lin_matrix<T, V>::get_const_col_indexed(size_t, typename V::iterator, size_t, size_t) [with T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; beachmat::const_col_indexed_info<V> = std::tuple<long long unsigned int, int*, double*>; typename V::iterator = double*; size_t = long long unsigned int; typename V::iterator = double*]':
numeric_matrix.cpp:90:1:   required from here
LIN_methods.h:58:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (indices.size()!=this->get_nrow()) {
                       ^
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:97:5:   required from 'void beachmat::general_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:90:1:   required from here
Csparse_matrix.h:201:34: 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:103:5:   required from 'void beachmat::general_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:90:1:   required from here
Csparse_matrix.h:201:34: 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:109:24:   required from 'T beachmat::general_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:90:1:   required from here
Csparse_matrix.h:114:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (loc!=iend && *loc==r) { 
                          ^
In file included from delayed_methods.h:2:0,
                 from delayed_matrix.h:109,
                 from Input_matrix.h:14,
                 from LIN_matrix.h:4,
                 from numeric_matrix.h:4,
                 from numeric_matrix.cpp:1:
unknown_matrix.h: In instantiation of 'void beachmat::unknown_matrix<T, V>::update_storage_by_row(size_t) [with T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; size_t = long long unsigned int]':
unknown_matrix.h:92:28:   required from 'void beachmat::unknown_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:97:5:   required from 'void beachmat::general_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::unknown_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:90:1:   required from here
unknown_matrix.h:65:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (r < row_indices[0] || r >= row_indices[1]) {
                                 ^
unknown_matrix.h:65:11: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (r < row_indices[0] || r >= row_indices[1]) {
           ^
unknown_matrix.h: In instantiation of 'void beachmat::unknown_matrix<T, V>::update_storage_by_col(size_t) [with T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; size_t = long long unsigned int]':
unknown_matrix.h:102:28:   required from 'void beachmat::unknown_matrix<T, V>::get_col(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:85:5:   required from 'void beachmat::general_lin_matrix<T, V, M>::get_col(size_t, Rcpp::Vector<13>::iterator, size_t, size_t) [with T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; M = beachmat::unknown_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:90:1:   required from here
unknown_matrix.h:74:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (c < col_indices[0] || c >= col_indices[1]) {
                                 ^
unknown_matrix.h:74:11: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (c < col_indices[0] || c >= col_indices[1]) {
           ^
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>::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:195:34:   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:97:5:   required from 'void beachmat::general_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:90:1:   required from here
Csparse_matrix.h:157:43: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             if (curdex!=*pIt && i[curdex] < r) { 
                                           ^
Csparse_matrix.h:164:45: 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˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include"   -I"C:/extsoft/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˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include"   -I"C:/extsoft/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˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include"   -I"C:/extsoft/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˜1.7-B/R/library/Rhdf5lib/lib/x64 -lhdf5_cpp -lhdf5 -lszip -lz -lpsapi -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/x64 -lR -lm -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.7-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˜1.7-B/R/library/Rhdf5lib/lib/x64 -lhdf5_cpp -lhdf5 -lszip -lz -lpsapi   -LC:/Users/BIOCBU˜1/BBS-3˜1.7-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-3.7-bioc/meat/beachmat.buildbin-libdir/beachmat/lib/x64" "C:/Users/biocbuild/bbs-3.7-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 delayed_matrix.h delayed_methods.h unknown_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-3.7-bioc/meat/beachmat.buildbin-libdir/beachmat/include/beachmat"
mv libbeachmat.* "C:/Users/biocbuild/bbs-3.7-bioc/meat/beachmat.buildbin-libdir/beachmat/lib/x64"
installing to C:/Users/biocbuild/bbs-3.7-bioc/meat/beachmat.buildbin-libdir/beachmat/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'beachmat' as beachmat_1.2.1.zip
* DONE (beachmat)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'beachmat' successfully unpacked and MD5 sums checked
In R CMD INSTALL

R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)

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 on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(beachmat)
> test_check("beachmat")
* checking for file 'C:\Users\biocbuild\bbs-3.7-bioc\R\library\beachmat\testpkg/DESCRIPTION' ... OK
* preparing 'beachtest':
* checking DESCRIPTION meta-information ... OK
* cleaning src
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* building 'beachtest_1.0.0.tar.gz'

* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpgFLzf7/beachtest.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using options '--no-manual --as-cran'
* checking for file 'beachtest/DESCRIPTION' ... OK
* this is package 'beachtest' version '1.0.0'
* 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 serialization versions ... OK
* checking whether package 'beachtest' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  9.4Mb
  sub-directories of 1Mb or more:
    libs   9.3Mb
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII 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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... NOTE
Registration problems:
  symbol 'cxxfun' not in namespace:
   .Call(cxxfun, test.mat)
  symbol 'cxxfun' not in namespace:
   .Call(cxxfun, test.mat, rx)
  symbol 'cxxfun' not in namespace:
   .Call(cxxfun, test.mat, it)
  symbol 'cxxfun' not in namespace:
   .Call(cxxfun, test.mat, i)
  symbol 'cxxfun' not in namespace:
   .Call(cxxfun, x, 0L)
  symbol 'cxxfun' not in namespace:
   .Call(cxxfun, x, 1L)
  symbol 'cxxfun' not in namespace:
   .Call(cxxfun, x, -1L)
  symbol 'cxxfun' not in namespace:
   .Call(cxxfun, x, 2L)
  symbol 'cxxfun' not in namespace:
   .Call(cxxfun, x, -2L)
  symbol 'cxxfun' not in namespace:
   .Call(cxxfun, x, 3L)
  symbol 'cxxfun' not in namespace:
   .Call(cxxfun, x, -3L)
  symbol 'cxxfun' not in namespace:
   .Call(cxxfun, x, 0L)
  symbol 'cxxfun' not in namespace:
   .Call(cxxfun, x, 1L)
  symbol 'cxxfun' not in namespace:
   .Call(cxxfun, x, -1L)
  symbol 'cxxfun' not in namespace:
   .Call(cxxfun, x, 2L)
  symbol 'cxxfun' not in namespace:
   .Call(cxxfun, x, -2L)
  symbol 'cxxfun' not in namespace:
   .Call(cxxfun, x, 3L)
  symbol 'cxxfun' not in namespace:
   .Call(cxxfun, x, -3L)
  symbol 'cxxfun' not in namespace:
   .Call(cxxfun, x, 4L)
  symbol 'cxxfun' not in namespace:
   .Call(cxxfun, x, -4L)
  symbol 'cxxfun' not in namespace:
   .Call(cxxfun, x, 5L)
  symbol 'cxxfun' not in namespace:
   .Call(cxxfun, x, -5L)
  symbol 'cxxfun' not in namespace:
   .Call(cxxfun, x, 6L)
  symbol 'cxxfun' not in namespace:
   .Call(cxxfun, x, -6L)
  symbol 'cxxfun' not in namespace:
   .Call(cxxfun, mats[[i]], 1L, NULL)
  symbol 'cxxfun' not in namespace:
   .Call(cxxfun, test.mat)
  symbol 'cxxfun' not in namespace:
   .Call(cxxfun, test.mat, rx)
  symbol 'cxxfun' not in namespace:
   .Call(cxxfun, test.mat, it, ordering)
  symbol 'cxxfun' not in namespace:
   .Call(cxxfun, test.mat, it, c, subr)
  symbol 'cxxfun' not in namespace:
   .Call(cxxfun, test.mat, it, r, subc)
  symbol 'cxxfun' not in namespace:
   .Call(cxxfun, test.mat, i, ordering)
  symbol 'cxxfun' not in namespace:
   .Call(cxxfun, test.mat, it, rx, ry)
  symbol 'cxxfun' not in namespace:
   .Call(cxxfun, test.mat, i, rx, ry)
See chapter 'System and foreign language interfaces' in the 'Writing R
Extensions' manual.
* checking R code for possible problems ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  'check_character_const_mat' 'check_character_const_slice'
  'check_character_edge_errors' 'check_character_edge_output_errors'
  'check_character_indexed_mat' 'check_character_indexed_slice'
  'check_character_mat' 'check_character_order'
  'check_character_output_indexed' 'check_character_output_mat'
  'check_character_output_slice' 'check_character_slice'
  'check_integer_const_mat' 'check_integer_const_slice'
  'check_integer_conversion' 'check_integer_converted_output'
  'check_integer_edge_errors' 'check_integer_edge_output_errors'
  'check_integer_indexed_mat' 'check_integer_indexed_slice'
  'check_integer_mat' 'check_integer_order'
  'check_integer_output_indexed' 'check_integer_output_mat'
  'check_integer_output_slice' 'check_integer_slice'
  'check_logical_const_mat' 'check_logical_const_slice'
  'check_logical_conversion' 'check_logical_converted_output'
  'check_logical_edge_errors' 'check_logical_edge_output_errors'
  'check_logical_indexed_mat' 'check_logical_indexed_slice'
  'check_logical_mat' 'check_logical_order'
  'check_logical_output_indexed' 'check_logical_output_mat'
  'check_logical_output_slice' 'check_logical_slice'
  'check_numeric_const_mat' 'check_numeric_const_slice'
  'check_numeric_conversion' 'check_numeric_converted_output'
  'check_numeric_edge_errors' 'check_numeric_edge_output_errors'
  'check_numeric_indexed_mat' 'check_numeric_indexed_slice'
  'check_numeric_mat' 'check_numeric_order'
  'check_numeric_output_indexed' 'check_numeric_output_mat'
  'check_numeric_output_slice' 'check_numeric_slice'
  'check_output_mode' 'check_type' 'delayed_funs'
All user-level objects in a package should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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 pragmas in C/C++ headers and code ... OK
* checking compilation flags used ... OK
* checking compiled code ... NOTE
File 'beachtest/libs/x64/beachtest.dll':
  Found no calls to: 'R_registerRoutines', 'R_useDynamicSymbols'

It is good practice to register native routines and to disable symbol
search.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking examples ... NONE
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R' [89s]
 OK
** running tests for arch 'x64' ...
  Running 'testthat.R' [97s]
 OK
* DONE

Status: 1 WARNING, 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpgFLzf7/beachtest.Rcheck/00check.log'
for details.


== testthat results  ===========================================================
OK: 109 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
   6.39    0.68  410.50 

R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

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 on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(beachmat)
> test_check("beachmat")
* checking for file 'C:\Users\biocbuild\bbs-3.7-bioc\R\library\beachmat\testpkg/DESCRIPTION' ... OK
* preparing 'beachtest':
* checking DESCRIPTION meta-information ... OK
* cleaning src
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* building 'beachtest_1.0.0.tar.gz'

* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpW8mVTQ/beachtest.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using options '--no-manual --as-cran'
* checking for file 'beachtest/DESCRIPTION' ... OK
* this is package 'beachtest' version '1.0.0'
* 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 serialization versions ... OK
* checking whether package 'beachtest' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  9.4Mb
  sub-directories of 1Mb or more:
    libs   9.3Mb
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII 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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... NOTE
Registration problems:
  symbol 'cxxfun' not in namespace:
   .Call(cxxfun, test.mat)
  symbol 'cxxfun' not in namespace:
   .Call(cxxfun, test.mat, rx)
  symbol 'cxxfun' not in namespace:
   .Call(cxxfun, test.mat, it)
  symbol 'cxxfun' not in namespace:
   .Call(cxxfun, test.mat, i)
  symbol 'cxxfun' not in namespace:
   .Call(cxxfun, x, 0L)
  symbol 'cxxfun' not in namespace:
   .Call(cxxfun, x, 1L)
  symbol 'cxxfun' not in namespace:
   .Call(cxxfun, x, -1L)
  symbol 'cxxfun' not in namespace:
   .Call(cxxfun, x, 2L)
  symbol 'cxxfun' not in namespace:
   .Call(cxxfun, x, -2L)
  symbol 'cxxfun' not in namespace:
   .Call(cxxfun, x, 3L)
  symbol 'cxxfun' not in namespace:
   .Call(cxxfun, x, -3L)
  symbol 'cxxfun' not in namespace:
   .Call(cxxfun, x, 0L)
  symbol 'cxxfun' not in namespace:
   .Call(cxxfun, x, 1L)
  symbol 'cxxfun' not in namespace:
   .Call(cxxfun, x, -1L)
  symbol 'cxxfun' not in namespace:
   .Call(cxxfun, x, 2L)
  symbol 'cxxfun' not in namespace:
   .Call(cxxfun, x, -2L)
  symbol 'cxxfun' not in namespace:
   .Call(cxxfun, x, 3L)
  symbol 'cxxfun' not in namespace:
   .Call(cxxfun, x, -3L)
  symbol 'cxxfun' not in namespace:
   .Call(cxxfun, x, 4L)
  symbol 'cxxfun' not in namespace:
   .Call(cxxfun, x, -4L)
  symbol 'cxxfun' not in namespace:
   .Call(cxxfun, x, 5L)
  symbol 'cxxfun' not in namespace:
   .Call(cxxfun, x, -5L)
  symbol 'cxxfun' not in namespace:
   .Call(cxxfun, x, 6L)
  symbol 'cxxfun' not in namespace:
   .Call(cxxfun, x, -6L)
  symbol 'cxxfun' not in namespace:
   .Call(cxxfun, mats[[i]], 1L, NULL)
  symbol 'cxxfun' not in namespace:
   .Call(cxxfun, test.mat)
  symbol 'cxxfun' not in namespace:
   .Call(cxxfun, test.mat, rx)
  symbol 'cxxfun' not in namespace:
   .Call(cxxfun, test.mat, it, ordering)
  symbol 'cxxfun' not in namespace:
   .Call(cxxfun, test.mat, it, c, subr)
  symbol 'cxxfun' not in namespace:
   .Call(cxxfun, test.mat, it, r, subc)
  symbol 'cxxfun' not in namespace:
   .Call(cxxfun, test.mat, i, ordering)
  symbol 'cxxfun' not in namespace:
   .Call(cxxfun, test.mat, it, rx, ry)
  symbol 'cxxfun' not in namespace:
   .Call(cxxfun, test.mat, i, rx, ry)
See chapter 'System and foreign language interfaces' in the 'Writing R
Extensions' manual.
* checking R code for possible problems ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  'check_character_const_mat' 'check_character_const_slice'
  'check_character_edge_errors' 'check_character_edge_output_errors'
  'check_character_indexed_mat' 'check_character_indexed_slice'
  'check_character_mat' 'check_character_order'
  'check_character_output_indexed' 'check_character_output_mat'
  'check_character_output_slice' 'check_character_slice'
  'check_integer_const_mat' 'check_integer_const_slice'
  'check_integer_conversion' 'check_integer_converted_output'
  'check_integer_edge_errors' 'check_integer_edge_output_errors'
  'check_integer_indexed_mat' 'check_integer_indexed_slice'
  'check_integer_mat' 'check_integer_order'
  'check_integer_output_indexed' 'check_integer_output_mat'
  'check_integer_output_slice' 'check_integer_slice'
  'check_logical_const_mat' 'check_logical_const_slice'
  'check_logical_conversion' 'check_logical_converted_output'
  'check_logical_edge_errors' 'check_logical_edge_output_errors'
  'check_logical_indexed_mat' 'check_logical_indexed_slice'
  'check_logical_mat' 'check_logical_order'
  'check_logical_output_indexed' 'check_logical_output_mat'
  'check_logical_output_slice' 'check_logical_slice'
  'check_numeric_const_mat' 'check_numeric_const_slice'
  'check_numeric_conversion' 'check_numeric_converted_output'
  'check_numeric_edge_errors' 'check_numeric_edge_output_errors'
  'check_numeric_indexed_mat' 'check_numeric_indexed_slice'
  'check_numeric_mat' 'check_numeric_order'
  'check_numeric_output_indexed' 'check_numeric_output_mat'
  'check_numeric_output_slice' 'check_numeric_slice'
  'check_output_mode' 'check_type' 'delayed_funs'
All user-level objects in a package should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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 pragmas in C/C++ headers and code ... OK
* checking compilation flags used ... OK
* checking compiled code ... NOTE
File 'beachtest/libs/x64/beachtest.dll':
  Found no calls to: 'R_registerRoutines', 'R_useDynamicSymbols'

It is good practice to register native routines and to disable symbol
search.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking examples ... NONE
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R' [103s]
 OK
** running tests for arch 'x64' ...
  Running 'testthat.R' [126s]
 OK
* DONE

Status: 1 WARNING, 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpW8mVTQ/beachtest.Rcheck/00check.log'
for details.


== testthat results  ===========================================================
OK: 109 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
   7.81    0.64  454.90