Package: beachmat

Version: 1.4.0

Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:beachmat.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings beachmat_1.4.0.tar.gz

StartedAt: 2019-04-15 22:24:05 -0400 (Mon, 15 Apr 2019)

EndedAt: 2019-04-15 22:25:29 -0400 (Mon, 15 Apr 2019)

EllapsedTime: 84.5 seconds

RetCode: 0

Status:  OK

CheckDir: beachmat.Rcheck

Warnings: 0

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### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:beachmat.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings beachmat_1.4.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/beachmat.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘beachmat/DESCRIPTION’ ... OK
* this is package ‘beachmat’ version ‘1.4.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘beachmat’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 69.5Mb
  sub-directories of 1Mb or more:
    lib   44.4Mb
    libs  24.4Mb
* 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
* 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 is not available
File ‘/home/biocbuild/bbs-3.8-bioc/R/library/beachmat/libs/beachmat.so’:
  Found ‘_ZSt4cerr’, possibly from ‘std::cerr’ (C++)
  Found ‘abort’, possibly from ‘abort’ (C)
  Found ‘exit’, possibly from ‘exit’ (C)
  Found ‘rand_r’, possibly from ‘rand_r’ (C)
  Found ‘stderr’, possibly from ‘stderr’ (C)
  Found ‘stdout’, possibly from ‘stdout’ (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 ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  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
  ‘/home/biocbuild/bbs-3.8-bioc/meat/beachmat.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL beachmat
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* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’
* installing *source* package ‘beachmat’ ...
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include" -I/usr/local/include   -fpic  -g -O2 -Wall -c HDF5_utils.cpp -o HDF5_utils.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include" -I/usr/local/include   -fpic  -g -O2 -Wall -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:43:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (indices.size()!=this->get_nrow()) {
                       ^
In file included from all_readers.h:8:0,
                 from character_matrix.h:4,
                 from character_matrix.cpp:1:
simple_reader.h: In instantiation of ‘beachmat::simple_reader<T, V>::simple_reader(const RObject&) [with T = Rcpp::String; V = Rcpp::Vector<16>; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’:
character_matrix.h:60:78:   required from ‘beachmat::general_character_matrix<RDR>::general_character_matrix(const RObject&) [with RDR = beachmat::simple_reader<Rcpp::String, Rcpp::Vector<16> >; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
character_matrix.cpp:52:119:   required from here
simple_reader.h:59:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (mat.size()!=(this->nrow)*NC) {
                   ^
In file included from all_readers.h:12:0,
                 from character_matrix.h:4,
                 from character_matrix.cpp:1:
delayed_reader.h: In instantiation of ‘static void beachmat::delayed_coord_transformer<T, V>::obtain_indices(const RObject&, size_t, bool&, size_t&, std::vector<long unsigned int>&) [with T = Rcpp::String; V = Rcpp::Vector<16>; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>; size_t = long unsigned int]’:
delayed_reader.h:115:19:   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_reader.h:371:20:   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:60:78:   required from ‘beachmat::general_character_matrix<RDR>::general_character_matrix(const RObject&) [with RDR = beachmat::delayed_matrix<Rcpp::String, Rcpp::Vector<16>, beachmat::character_matrix>; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
character_matrix.cpp:165:91:   required from here
delayed_reader.h:154:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (i < 1 || i > original_dim) {
                        ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include" -I/usr/local/include   -fpic  -g -O2 -Wall -c character_output.cpp -o character_output.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include" -I/usr/local/include   -fpic  -g -O2 -Wall -c dim_checker.cpp -o dim_checker.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include" -I/usr/local/include   -fpic  -g -O2 -Wall -c find_chunks.cpp -o find_chunks.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include" -I/usr/local/include   -fpic  -g -O2 -Wall -c functions.cpp -o functions.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include" -I/usr/local/include   -fpic  -g -O2 -Wall -c integer_matrix.cpp -o integer_matrix.o
In file included from all_readers.h:8:0,
                 from LIN_matrix.h:4,
                 from integer_matrix.h:4,
                 from integer_matrix.cpp:1:
simple_reader.h: In instantiation of ‘beachmat::simple_reader<T, V>::simple_reader(const RObject&) [with T = int; V = Rcpp::Vector<13>; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’:
LIN_methods_read.h:92:99:   required from ‘beachmat::general_lin_matrix<T, V, RDR>::general_lin_matrix(const RObject&) [with T = int; V = Rcpp::Vector<13>; RDR = beachmat::simple_reader<int, Rcpp::Vector<13> >; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
LIN_methods_read.h:181:100:   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_reader.h:59:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (mat.size()!=(this->nrow)*NC) {
                   ^
In file included from all_readers.h:12:0,
                 from LIN_matrix.h:4,
                 from integer_matrix.h:4,
                 from integer_matrix.cpp:1:
delayed_reader.h: In instantiation of ‘static void beachmat::delayed_coord_transformer<T, V>::obtain_indices(const RObject&, size_t, bool&, size_t&, std::vector<long unsigned int>&) [with T = int; V = Rcpp::Vector<13>; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>; size_t = long unsigned int]’:
delayed_reader.h:115:19:   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_reader.h:371:20:   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_read.h:92:99:   required from ‘beachmat::general_lin_matrix<T, V, RDR>::general_lin_matrix(const RObject&) [with T = int; V = Rcpp::Vector<13>; RDR = beachmat::delayed_matrix<int, Rcpp::Vector<13>, beachmat::lin_matrix<int, Rcpp::Vector<13> > >; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
integer_matrix.cpp:43:87:   required from here
delayed_reader.h:154:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (i < 1 || i > original_dim) {
                        ^
In file included from LIN_matrix.h:238:0,
                 from integer_matrix.h:4,
                 from integer_matrix.cpp:1:
LIN_methods_read.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 unsigned int, int*, int*>; typename V::iterator = int*; size_t = long unsigned int; typename V::iterator = int*]’:
integer_matrix.cpp:70:1:   required from here
LIN_methods_read.h:82:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (indices.size()!=this->get_nrow()) {
                       ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include" -I/usr/local/include   -fpic  -g -O2 -Wall -c logical_matrix.cpp -o logical_matrix.o
In file included from all_readers.h:9:0,
                 from LIN_matrix.h:4,
                 from logical_matrix.h:4,
                 from logical_matrix.cpp:1:
dense_reader.h: In instantiation of ‘beachmat::dense_reader<T, V>::dense_reader(const RObject&) [with T = int; V = Rcpp::Vector<10, Rcpp::PreserveStorage>; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’:
LIN_methods_read.h:92:99:   required from ‘beachmat::general_lin_matrix<T, V, RDR>::general_lin_matrix(const RObject&) [with T = int; V = Rcpp::Vector<10, Rcpp::PreserveStorage>; RDR = beachmat::dense_reader<int, Rcpp::Vector<10, Rcpp::PreserveStorage> >; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
LIN_methods_read.h:196:97:   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_reader.h:60:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (x.size()!=(this->nrow)*NC) {
                 ^
In file included from all_readers.h:10:0,
                 from LIN_matrix.h:4,
                 from logical_matrix.h:4,
                 from logical_matrix.cpp:1:
Csparse_reader.h: In instantiation of ‘beachmat::Csparse_reader<T, V>::Csparse_reader(const RObject&) [with T = int; V = Rcpp::Vector<10, Rcpp::PreserveStorage>; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’:
LIN_methods_read.h:92:99:   required from ‘beachmat::general_lin_matrix<T, V, RDR>::general_lin_matrix(const RObject&) [with T = int; V = Rcpp::Vector<10, Rcpp::PreserveStorage>; RDR = beachmat::Csparse_reader<int, Rcpp::Vector<10, Rcpp::PreserveStorage> >; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
LIN_methods_read.h:211:103:   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_reader.h:78:13: 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_reader.h:106:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (curi<0 || curi>=NR) {
                           ^
In file included from all_readers.h:8:0,
                 from LIN_matrix.h:4,
                 from logical_matrix.h:4,
                 from logical_matrix.cpp:1:
simple_reader.h: In instantiation of ‘beachmat::simple_reader<T, V>::simple_reader(const RObject&) [with T = int; V = Rcpp::Vector<10, Rcpp::PreserveStorage>; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’:
LIN_methods_read.h:92:99:   required from ‘beachmat::general_lin_matrix<T, V, RDR>::general_lin_matrix(const RObject&) [with T = int; V = Rcpp::Vector<10, Rcpp::PreserveStorage>; RDR = beachmat::simple_reader<int, Rcpp::Vector<10, Rcpp::PreserveStorage> >; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
LIN_methods_read.h:181:100:   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:63:78:   required from here
simple_reader.h:59:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (mat.size()!=(this->nrow)*NC) {
                   ^
In file included from all_readers.h:12:0,
                 from LIN_matrix.h:4,
                 from logical_matrix.h:4,
                 from logical_matrix.cpp:1:
delayed_reader.h: In instantiation of ‘static void beachmat::delayed_coord_transformer<T, V>::obtain_indices(const RObject&, size_t, bool&, size_t&, std::vector<long unsigned int>&) [with T = int; V = Rcpp::Vector<10, Rcpp::PreserveStorage>; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>; size_t = long unsigned int]’:
delayed_reader.h:115:19:   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_reader.h:371:20:   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_read.h:92:99:   required from ‘beachmat::general_lin_matrix<T, V, RDR>::general_lin_matrix(const RObject&) [with T = int; V = Rcpp::Vector<10, Rcpp::PreserveStorage>; RDR = 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:57:87:   required from here
delayed_reader.h:154:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (i < 1 || i > original_dim) {
                        ^
In file included from LIN_matrix.h:238:0,
                 from logical_matrix.h:4,
                 from logical_matrix.cpp:1:
LIN_methods_read.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 unsigned int, int*, int*>; typename V::iterator = int*; size_t = long unsigned int; typename V::iterator = int*]’:
logical_matrix.cpp:86:1:   required from here
LIN_methods_read.h:82:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (indices.size()!=this->get_nrow()) {
                       ^
In file included from all_readers.h:10:0,
                 from LIN_matrix.h:4,
                 from logical_matrix.h:4,
                 from logical_matrix.cpp:1:
Csparse_reader.h: In instantiation of ‘void beachmat::Csparse_reader<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 unsigned int]’:
LIN_methods_read.h:120:5:   required from ‘void beachmat::general_lin_matrix<T, V, RDR>::get_row(size_t, Rcpp::Vector<13>::iterator, size_t, size_t) [with T = int; V = Rcpp::Vector<10, Rcpp::PreserveStorage>; RDR = beachmat::Csparse_reader<int, Rcpp::Vector<10, Rcpp::PreserveStorage> >; size_t = long unsigned int; Rcpp::Vector<13>::iterator = int*; Rcpp::traits::storage_type<13>::type = int]’
logical_matrix.cpp:86:1:   required from here
Csparse_reader.h:208:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (idex!=*pIt && i[idex]==r) { (*out)=x[idex]; }
                                  ^
Csparse_reader.h: In instantiation of ‘void beachmat::Csparse_reader<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 unsigned int]’:
LIN_methods_read.h:126:5:   required from ‘void beachmat::general_lin_matrix<T, V, RDR>::get_row(size_t, Rcpp::Vector<14, Rcpp::PreserveStorage>::iterator, size_t, size_t) [with T = int; V = Rcpp::Vector<10, Rcpp::PreserveStorage>; RDR = beachmat::Csparse_reader<int, Rcpp::Vector<10, Rcpp::PreserveStorage> >; size_t = long unsigned int; Rcpp::Vector<14, Rcpp::PreserveStorage>::iterator = double*; Rcpp::traits::storage_type<14>::type = double]’
logical_matrix.cpp:86:1:   required from here
Csparse_reader.h:208:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Csparse_reader.h: In instantiation of ‘T beachmat::Csparse_reader<T, V>::get(size_t, size_t) [with T = int; V = Rcpp::Vector<10, Rcpp::PreserveStorage>; size_t = long unsigned int]’:
LIN_methods_read.h:132:27:   required from ‘T beachmat::general_lin_matrix<T, V, RDR>::get(size_t, size_t) [with T = int; V = Rcpp::Vector<10, Rcpp::PreserveStorage>; RDR = beachmat::Csparse_reader<int, Rcpp::Vector<10, Rcpp::PreserveStorage> >; size_t = long unsigned int]’
logical_matrix.cpp:86:1:   required from here
Csparse_reader.h:121:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (loc!=iend && *loc==r) { 
                          ^
Csparse_reader.h: In instantiation of ‘void beachmat::Csparse_reader<T, V>::update_indices(size_t, size_t, size_t) [with T = int; V = Rcpp::Vector<10, Rcpp::PreserveStorage>; size_t = long unsigned int]’:
Csparse_reader.h:202:19:   required from ‘void beachmat::Csparse_reader<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 unsigned int]’
LIN_methods_read.h:120:5:   required from ‘void beachmat::general_lin_matrix<T, V, RDR>::get_row(size_t, Rcpp::Vector<13>::iterator, size_t, size_t) [with T = int; V = Rcpp::Vector<10, Rcpp::PreserveStorage>; RDR = beachmat::Csparse_reader<int, Rcpp::Vector<10, Rcpp::PreserveStorage> >; size_t = long unsigned int; Rcpp::Vector<13>::iterator = int*; Rcpp::traits::storage_type<13>::type = int]’
logical_matrix.cpp:86:1:   required from here
Csparse_reader.h:164:43: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             if (curdex!=*pIt && i[curdex] < r) { 
                                           ^
Csparse_reader.h:171:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             if (curdex!=*pIt && i[curdex-1] >= r) { 
                                             ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include" -I/usr/local/include   -fpic  -g -O2 -Wall -c numeric_matrix.cpp -o numeric_matrix.o
In file included from all_readers.h:9:0,
                 from LIN_matrix.h:4,
                 from numeric_matrix.h:4,
                 from numeric_matrix.cpp:1:
dense_reader.h: In instantiation of ‘beachmat::dense_reader<T, V>::dense_reader(const RObject&) [with T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’:
LIN_methods_read.h:92:99:   required from ‘beachmat::general_lin_matrix<T, V, RDR>::general_lin_matrix(const RObject&) [with T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; RDR = beachmat::dense_reader<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
LIN_methods_read.h:196:97:   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_reader.h:60:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (x.size()!=(this->nrow)*NC) {
                 ^
In file included from all_readers.h:10:0,
                 from LIN_matrix.h:4,
                 from numeric_matrix.h:4,
                 from numeric_matrix.cpp:1:
Csparse_reader.h: In instantiation of ‘beachmat::Csparse_reader<T, V>::Csparse_reader(const RObject&) [with T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’:
LIN_methods_read.h:92:99:   required from ‘beachmat::general_lin_matrix<T, V, RDR>::general_lin_matrix(const RObject&) [with T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; RDR = beachmat::Csparse_reader<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
LIN_methods_read.h:211:103:   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_reader.h:78:13: 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_reader.h:106:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (curi<0 || curi>=NR) {
                           ^
In file included from all_readers.h:8:0,
                 from LIN_matrix.h:4,
                 from numeric_matrix.h:4,
                 from numeric_matrix.cpp:1:
simple_reader.h: In instantiation of ‘beachmat::simple_reader<T, V>::simple_reader(const RObject&) [with T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’:
LIN_methods_read.h:92:99:   required from ‘beachmat::general_lin_matrix<T, V, RDR>::general_lin_matrix(const RObject&) [with T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; RDR = beachmat::simple_reader<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
LIN_methods_read.h:181:100:   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:63:78:   required from here
simple_reader.h:59:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (mat.size()!=(this->nrow)*NC) {
                   ^
In file included from all_readers.h:12:0,
                 from LIN_matrix.h:4,
                 from numeric_matrix.h:4,
                 from numeric_matrix.cpp:1:
delayed_reader.h: In instantiation of ‘static void beachmat::delayed_coord_transformer<T, V>::obtain_indices(const RObject&, size_t, bool&, size_t&, std::vector<long unsigned int>&) [with T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>; size_t = long unsigned int]’:
delayed_reader.h:115:19:   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_reader.h:371:20:   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_read.h:92:99:   required from ‘beachmat::general_lin_matrix<T, V, RDR>::general_lin_matrix(const RObject&) [with T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; RDR = 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:57:87:   required from here
delayed_reader.h:154:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (i < 1 || i > original_dim) {
                        ^
In file included from LIN_matrix.h:238:0,
                 from numeric_matrix.h:4,
                 from numeric_matrix.cpp:1:
LIN_methods_read.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 unsigned int, int*, double*>; typename V::iterator = double*; size_t = long unsigned int; typename V::iterator = double*]’:
numeric_matrix.cpp:86:1:   required from here
LIN_methods_read.h:82:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (indices.size()!=this->get_nrow()) {
                       ^
In file included from all_readers.h:10:0,
                 from LIN_matrix.h:4,
                 from numeric_matrix.h:4,
                 from numeric_matrix.cpp:1:
Csparse_reader.h: In instantiation of ‘void beachmat::Csparse_reader<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 unsigned int]’:
LIN_methods_read.h:120:5:   required from ‘void beachmat::general_lin_matrix<T, V, RDR>::get_row(size_t, Rcpp::Vector<13>::iterator, size_t, size_t) [with T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; RDR = beachmat::Csparse_reader<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >; size_t = long unsigned int; Rcpp::Vector<13>::iterator = int*; Rcpp::traits::storage_type<13>::type = int]’
numeric_matrix.cpp:86:1:   required from here
Csparse_reader.h:208:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (idex!=*pIt && i[idex]==r) { (*out)=x[idex]; }
                                  ^
Csparse_reader.h: In instantiation of ‘void beachmat::Csparse_reader<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 unsigned int]’:
LIN_methods_read.h:126:5:   required from ‘void beachmat::general_lin_matrix<T, V, RDR>::get_row(size_t, Rcpp::Vector<14, Rcpp::PreserveStorage>::iterator, size_t, size_t) [with T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; RDR = beachmat::Csparse_reader<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >; size_t = long unsigned int; Rcpp::Vector<14, Rcpp::PreserveStorage>::iterator = double*; Rcpp::traits::storage_type<14>::type = double]’
numeric_matrix.cpp:86:1:   required from here
Csparse_reader.h:208:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Csparse_reader.h: In instantiation of ‘T beachmat::Csparse_reader<T, V>::get(size_t, size_t) [with T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; size_t = long unsigned int]’:
LIN_methods_read.h:132:27:   required from ‘T beachmat::general_lin_matrix<T, V, RDR>::get(size_t, size_t) [with T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; RDR = beachmat::Csparse_reader<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >; size_t = long unsigned int]’
numeric_matrix.cpp:86:1:   required from here
Csparse_reader.h:121:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (loc!=iend && *loc==r) { 
                          ^
Csparse_reader.h: In instantiation of ‘void beachmat::Csparse_reader<T, V>::update_indices(size_t, size_t, size_t) [with T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; size_t = long unsigned int]’:
Csparse_reader.h:202:19:   required from ‘void beachmat::Csparse_reader<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 unsigned int]’
LIN_methods_read.h:120:5:   required from ‘void beachmat::general_lin_matrix<T, V, RDR>::get_row(size_t, Rcpp::Vector<13>::iterator, size_t, size_t) [with T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; RDR = beachmat::Csparse_reader<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >; size_t = long unsigned int; Rcpp::Vector<13>::iterator = int*; Rcpp::traits::storage_type<13>::type = int]’
numeric_matrix.cpp:86:1:   required from here
Csparse_reader.h:164:43: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             if (curdex!=*pIt && i[curdex] < r) { 
                                           ^
Csparse_reader.h:171:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             if (curdex!=*pIt && i[curdex-1] >= r) { 
                                             ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include" -I/usr/local/include   -fpic  -g -O2 -Wall -c output_param.cpp -o output_param.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include" -I/usr/local/include   -fpic  -g -O2 -Wall -c repacker.cpp -o repacker.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include" -I/usr/local/include   -fpic  -g -O2 -Wall -c utils.cpp -o utils.o
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.8-bioc/R/lib -L/usr/local/lib -o beachmat.so HDF5_utils.o character_matrix.o character_output.o dim_checker.o find_chunks.o functions.o integer_matrix.o logical_matrix.o numeric_matrix.o output_param.o repacker.o utils.o /home/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/lib/libhdf5_cpp.a /home/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/lib/libhdf5.a /home/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/lib/libsz.a -lz -L/home/biocbuild/bbs-3.8-bioc/R/lib -lR
ar rc libbeachmat.a dim_checker.o character_matrix.o character_output.o integer_matrix.o logical_matrix.o numeric_matrix.o utils.o HDF5_utils.o output_param.o
g++ -std=gnu++11 -shared -L/usr/local/lib -o libbeachmat.so dim_checker.o character_matrix.o character_output.o integer_matrix.o logical_matrix.o numeric_matrix.o utils.o HDF5_utils.o output_param.o `echo 'Rhdf5lib::pkgconfig("PKG_CXX_LIBS")'| "/home/biocbuild/bbs-3.8-bioc/R/bin/R" --vanilla --slave` 
mkdir -p "/home/biocbuild/bbs-3.8-bioc/R/library/beachmat/lib" "/home/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat"
cp dim_checker.h utils.h beachmat.h HDF5_utils.h output_param.h HDF5_reader.h Csparse_reader.h dense_reader.h simple_reader.h all_readers.h delayed_reader.h unknown_reader.h external_reader.h simple_writer.h Csparse_writer.h HDF5_writer.h all_writers.h LIN_matrix.h LIN_methods_read.h LIN_methods_write.h LIN_output.h logical_matrix.h integer_matrix.h character_matrix.h numeric_matrix.h character_output.h   "/home/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat"
mv libbeachmat.* "/home/biocbuild/bbs-3.8-bioc/R/library/beachmat/lib"
installing to /home/biocbuild/bbs-3.8-bioc/R/library/beachmat/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (beachmat)

R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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")
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 114 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  6.940   0.236   7.225 

name	user	system	elapsed
getBestChunkDims	0	0	0
pkgconfig	0.004	0.000	0.003
rechunkByMargins	0.404	0.024	0.597
supportCppAccess	1.124	0.060	1.189