Package: beachmat

Version: 1.2.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:beachmat.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings beachmat_1.2.1.tar.gz

StartedAt: 2018-10-16 20:02:42 -0400 (Tue, 16 Oct 2018)

EndedAt: 2018-10-16 20:07:32 -0400 (Tue, 16 Oct 2018)

EllapsedTime: 289.4 seconds

RetCode: 0

Status:  OK

CheckDir: beachmat.Rcheck

Warnings: 0

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:beachmat.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings beachmat_1.2.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/beachmat.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘beachmat’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 21.5Mb
  sub-directories of 1Mb or more:
    lib   16.0Mb
    libs   5.1Mb
* 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 ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/libs/beachmat.so’:
  Found ‘__ZNSt3__14cerrE’, possibly from ‘std::cerr’ (C++)
  Found ‘___stderrp’, possibly from ‘stderr’ (C)
  Found ‘___stdoutp’, possibly from ‘stdout’ (C)
  Found ‘_abort’, possibly from ‘abort’ (C)
  Found ‘_exit’, possibly from ‘exit’ (C)
  Found ‘_rand_r’, possibly from ‘rand_r’ (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
  ‘/Users/biocbuild/bbs-3.7-bioc/meat/beachmat.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL beachmat
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘beachmat’ ...
** libs
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c HDF5_utils.cpp -o HDF5_utils.o
In file included from HDF5_utils.cpp:1:
In file included from ./HDF5_utils.h:4:
In file included from ./beachmat.h:15:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Cpp.h:27:
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Attribute.h:106:13: warning: 'H5::Attribute::iterateAttrs' hides overloaded virtual function [-Woverloaded-virtual]
        int iterateAttrs() { return 0; }
            ^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Location.h:82:21: note: hidden overloaded virtual function 'H5::H5Location::iterateAttrs' declared here: different number of parameters (3 vs 0)
        virtual int iterateAttrs(attr_operator_t user_op, unsigned* idx = NULL, void* op_data = NULL);
                    ^
In file included from HDF5_utils.cpp:1:
In file included from ./HDF5_utils.h:4:
In file included from ./beachmat.h:15:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Cpp.h:27:
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Attribute.h:109:14: warning: 'H5::Attribute::renameAttr' hides overloaded virtual functions [-Woverloaded-virtual]
        void renameAttr() {}
             ^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Location.h:89:22: note: hidden overloaded virtual function 'H5::H5Location::renameAttr' declared here: different number of parameters (2 vs 0)
        virtual void renameAttr(const char* oldname, const char* newname) const;
                     ^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Location.h:90:22: note: hidden overloaded virtual function 'H5::H5Location::renameAttr' declared here: different number of parameters (2 vs 0)
        virtual void renameAttr(const H5std_string& oldname, const H5std_string& newname) const;
                     ^
2 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c any_matrix.cpp -o any_matrix.o
In file included from any_matrix.cpp:1:
In file included from ./any_matrix.h:4:
In file included from ./beachmat.h:15:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Cpp.h:27:
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Attribute.h:106:13: warning: 'H5::Attribute::iterateAttrs' hides overloaded virtual function [-Woverloaded-virtual]
        int iterateAttrs() { return 0; }
            ^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Location.h:82:21: note: hidden overloaded virtual function 'H5::H5Location::iterateAttrs' declared here: different number of parameters (3 vs 0)
        virtual int iterateAttrs(attr_operator_t user_op, unsigned* idx = NULL, void* op_data = NULL);
                    ^
In file included from any_matrix.cpp:1:
In file included from ./any_matrix.h:4:
In file included from ./beachmat.h:15:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Cpp.h:27:
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Attribute.h:109:14: warning: 'H5::Attribute::renameAttr' hides overloaded virtual functions [-Woverloaded-virtual]
        void renameAttr() {}
             ^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Location.h:89:22: note: hidden overloaded virtual function 'H5::H5Location::renameAttr' declared here: different number of parameters (2 vs 0)
        virtual void renameAttr(const char* oldname, const char* newname) const;
                     ^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Location.h:90:22: note: hidden overloaded virtual function 'H5::H5Location::renameAttr' declared here: different number of parameters (2 vs 0)
        virtual void renameAttr(const H5std_string& oldname, const H5std_string& newname) const;
                     ^
2 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c character_matrix.cpp -o character_matrix.o
In file included from character_matrix.cpp:1:
In file included from ./character_matrix.h:4:
In file included from ./Input_matrix.h:4:
In file included from ./beachmat.h:15:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Cpp.h:27:
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Attribute.h:106:13: warning: 'H5::Attribute::iterateAttrs' hides overloaded virtual function [-Woverloaded-virtual]
        int iterateAttrs() { return 0; }
            ^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Location.h:82:21: note: hidden overloaded virtual function 'H5::H5Location::iterateAttrs' declared here: different number of parameters (3 vs 0)
        virtual int iterateAttrs(attr_operator_t user_op, unsigned* idx = NULL, void* op_data = NULL);
                    ^
In file included from character_matrix.cpp:1:
In file included from ./character_matrix.h:4:
In file included from ./Input_matrix.h:4:
In file included from ./beachmat.h:15:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Cpp.h:27:
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Attribute.h:109:14: warning: 'H5::Attribute::renameAttr' hides overloaded virtual functions [-Woverloaded-virtual]
        void renameAttr() {}
             ^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Location.h:89:22: note: hidden overloaded virtual function 'H5::H5Location::renameAttr' declared here: different number of parameters (2 vs 0)
        virtual void renameAttr(const char* oldname, const char* newname) const;
                     ^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Location.h:90:22: note: hidden overloaded virtual function 'H5::H5Location::renameAttr' declared here: different number of parameters (2 vs 0)
        virtual void renameAttr(const H5std_string& oldname, const H5std_string& newname) const;
                     ^
2 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c character_output.cpp -o character_output.o
In file included from character_output.cpp:1:
In file included from ./character_output.h:4:
In file included from ./Output_matrix.h:4:
In file included from ./beachmat.h:15:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Cpp.h:27:
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Attribute.h:106:13: warning: 'H5::Attribute::iterateAttrs' hides overloaded virtual function [-Woverloaded-virtual]
        int iterateAttrs() { return 0; }
            ^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Location.h:82:21: note: hidden overloaded virtual function 'H5::H5Location::iterateAttrs' declared here: different number of parameters (3 vs 0)
        virtual int iterateAttrs(attr_operator_t user_op, unsigned* idx = NULL, void* op_data = NULL);
                    ^
In file included from character_output.cpp:1:
In file included from ./character_output.h:4:
In file included from ./Output_matrix.h:4:
In file included from ./beachmat.h:15:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Cpp.h:27:
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Attribute.h:109:14: warning: 'H5::Attribute::renameAttr' hides overloaded virtual functions [-Woverloaded-virtual]
        void renameAttr() {}
             ^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Location.h:89:22: note: hidden overloaded virtual function 'H5::H5Location::renameAttr' declared here: different number of parameters (2 vs 0)
        virtual void renameAttr(const char* oldname, const char* newname) const;
                     ^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Location.h:90:22: note: hidden overloaded virtual function 'H5::H5Location::renameAttr' declared here: different number of parameters (2 vs 0)
        virtual void renameAttr(const H5std_string& oldname, const H5std_string& newname) const;
                     ^
2 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c find_chunks.cpp -o find_chunks.o
In file included from find_chunks.cpp:1:
In file included from ./beachmat.h:15:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Cpp.h:27:
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Attribute.h:106:13: warning: 'H5::Attribute::iterateAttrs' hides overloaded virtual function [-Woverloaded-virtual]
        int iterateAttrs() { return 0; }
            ^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Location.h:82:21: note: hidden overloaded virtual function 'H5::H5Location::iterateAttrs' declared here: different number of parameters (3 vs 0)
        virtual int iterateAttrs(attr_operator_t user_op, unsigned* idx = NULL, void* op_data = NULL);
                    ^
In file included from find_chunks.cpp:1:
In file included from ./beachmat.h:15:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Cpp.h:27:
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Attribute.h:109:14: warning: 'H5::Attribute::renameAttr' hides overloaded virtual functions [-Woverloaded-virtual]
        void renameAttr() {}
             ^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Location.h:89:22: note: hidden overloaded virtual function 'H5::H5Location::renameAttr' declared here: different number of parameters (2 vs 0)
        virtual void renameAttr(const char* oldname, const char* newname) const;
                     ^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Location.h:90:22: note: hidden overloaded virtual function 'H5::H5Location::renameAttr' declared here: different number of parameters (2 vs 0)
        virtual void renameAttr(const H5std_string& oldname, const H5std_string& newname) const;
                     ^
2 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c functions.cpp -o functions.o
In file included from functions.cpp:1:
In file included from ./functions.h:4:
In file included from ./beachmat.h:15:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Cpp.h:27:
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Attribute.h:106:13: warning: 'H5::Attribute::iterateAttrs' hides overloaded virtual function [-Woverloaded-virtual]
        int iterateAttrs() { return 0; }
            ^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Location.h:82:21: note: hidden overloaded virtual function 'H5::H5Location::iterateAttrs' declared here: different number of parameters (3 vs 0)
        virtual int iterateAttrs(attr_operator_t user_op, unsigned* idx = NULL, void* op_data = NULL);
                    ^
In file included from functions.cpp:1:
In file included from ./functions.h:4:
In file included from ./beachmat.h:15:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Cpp.h:27:
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Attribute.h:109:14: warning: 'H5::Attribute::renameAttr' hides overloaded virtual functions [-Woverloaded-virtual]
        void renameAttr() {}
             ^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Location.h:89:22: note: hidden overloaded virtual function 'H5::H5Location::renameAttr' declared here: different number of parameters (2 vs 0)
        virtual void renameAttr(const char* oldname, const char* newname) const;
                     ^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Location.h:90:22: note: hidden overloaded virtual function 'H5::H5Location::renameAttr' declared here: different number of parameters (2 vs 0)
        virtual void renameAttr(const H5std_string& oldname, const H5std_string& newname) const;
                     ^
2 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c integer_matrix.cpp -o integer_matrix.o
In file included from integer_matrix.cpp:1:
In file included from ./integer_matrix.h:4:
In file included from ./LIN_matrix.h:4:
In file included from ./Input_matrix.h:4:
In file included from ./beachmat.h:15:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Cpp.h:27:
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Attribute.h:106:13: warning: 'H5::Attribute::iterateAttrs' hides overloaded virtual function [-Woverloaded-virtual]
        int iterateAttrs() { return 0; }
            ^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Location.h:82:21: note: hidden overloaded virtual function 'H5::H5Location::iterateAttrs' declared here: different number of parameters (3 vs 0)
        virtual int iterateAttrs(attr_operator_t user_op, unsigned* idx = NULL, void* op_data = NULL);
                    ^
In file included from integer_matrix.cpp:1:
In file included from ./integer_matrix.h:4:
In file included from ./LIN_matrix.h:4:
In file included from ./Input_matrix.h:4:
In file included from ./beachmat.h:15:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Cpp.h:27:
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Attribute.h:109:14: warning: 'H5::Attribute::renameAttr' hides overloaded virtual functions [-Woverloaded-virtual]
        void renameAttr() {}
             ^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Location.h:89:22: note: hidden overloaded virtual function 'H5::H5Location::renameAttr' declared here: different number of parameters (2 vs 0)
        virtual void renameAttr(const char* oldname, const char* newname) const;
                     ^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Location.h:90:22: note: hidden overloaded virtual function 'H5::H5Location::renameAttr' declared here: different number of parameters (2 vs 0)
        virtual void renameAttr(const H5std_string& oldname, const H5std_string& newname) const;
                     ^
2 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c logical_matrix.cpp -o logical_matrix.o
In file included from logical_matrix.cpp:1:
In file included from ./logical_matrix.h:4:
In file included from ./LIN_matrix.h:4:
In file included from ./Input_matrix.h:4:
In file included from ./beachmat.h:15:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Cpp.h:27:
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Attribute.h:106:13: warning: 'H5::Attribute::iterateAttrs' hides overloaded virtual function [-Woverloaded-virtual]
        int iterateAttrs() { return 0; }
            ^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Location.h:82:21: note: hidden overloaded virtual function 'H5::H5Location::iterateAttrs' declared here: different number of parameters (3 vs 0)
        virtual int iterateAttrs(attr_operator_t user_op, unsigned* idx = NULL, void* op_data = NULL);
                    ^
In file included from logical_matrix.cpp:1:
In file included from ./logical_matrix.h:4:
In file included from ./LIN_matrix.h:4:
In file included from ./Input_matrix.h:4:
In file included from ./beachmat.h:15:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Cpp.h:27:
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Attribute.h:109:14: warning: 'H5::Attribute::renameAttr' hides overloaded virtual functions [-Woverloaded-virtual]
        void renameAttr() {}
             ^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Location.h:89:22: note: hidden overloaded virtual function 'H5::H5Location::renameAttr' declared here: different number of parameters (2 vs 0)
        virtual void renameAttr(const char* oldname, const char* newname) const;
                     ^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Location.h:90:22: note: hidden overloaded virtual function 'H5::H5Location::renameAttr' declared here: different number of parameters (2 vs 0)
        virtual void renameAttr(const H5std_string& oldname, const H5std_string& newname) const;
                     ^
2 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c numeric_matrix.cpp -o numeric_matrix.o
In file included from numeric_matrix.cpp:1:
In file included from ./numeric_matrix.h:4:
In file included from ./LIN_matrix.h:4:
In file included from ./Input_matrix.h:4:
In file included from ./beachmat.h:15:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Cpp.h:27:
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Attribute.h:106:13: warning: 'H5::Attribute::iterateAttrs' hides overloaded virtual function [-Woverloaded-virtual]
        int iterateAttrs() { return 0; }
            ^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Location.h:82:21: note: hidden overloaded virtual function 'H5::H5Location::iterateAttrs' declared here: different number of parameters (3 vs 0)
        virtual int iterateAttrs(attr_operator_t user_op, unsigned* idx = NULL, void* op_data = NULL);
                    ^
In file included from numeric_matrix.cpp:1:
In file included from ./numeric_matrix.h:4:
In file included from ./LIN_matrix.h:4:
In file included from ./Input_matrix.h:4:
In file included from ./beachmat.h:15:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Cpp.h:27:
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Attribute.h:109:14: warning: 'H5::Attribute::renameAttr' hides overloaded virtual functions [-Woverloaded-virtual]
        void renameAttr() {}
             ^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Location.h:89:22: note: hidden overloaded virtual function 'H5::H5Location::renameAttr' declared here: different number of parameters (2 vs 0)
        virtual void renameAttr(const char* oldname, const char* newname) const;
                     ^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Location.h:90:22: note: hidden overloaded virtual function 'H5::H5Location::renameAttr' declared here: different number of parameters (2 vs 0)
        virtual void renameAttr(const H5std_string& oldname, const H5std_string& newname) const;
                     ^
2 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c output_param.cpp -o output_param.o
In file included from output_param.cpp:1:
In file included from ./output_param.h:4:
In file included from ./utils.h:4:
In file included from ./beachmat.h:15:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Cpp.h:27:
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Attribute.h:106:13: warning: 'H5::Attribute::iterateAttrs' hides overloaded virtual function [-Woverloaded-virtual]
        int iterateAttrs() { return 0; }
            ^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Location.h:82:21: note: hidden overloaded virtual function 'H5::H5Location::iterateAttrs' declared here: different number of parameters (3 vs 0)
        virtual int iterateAttrs(attr_operator_t user_op, unsigned* idx = NULL, void* op_data = NULL);
                    ^
In file included from output_param.cpp:1:
In file included from ./output_param.h:4:
In file included from ./utils.h:4:
In file included from ./beachmat.h:15:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Cpp.h:27:
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Attribute.h:109:14: warning: 'H5::Attribute::renameAttr' hides overloaded virtual functions [-Woverloaded-virtual]
        void renameAttr() {}
             ^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Location.h:89:22: note: hidden overloaded virtual function 'H5::H5Location::renameAttr' declared here: different number of parameters (2 vs 0)
        virtual void renameAttr(const char* oldname, const char* newname) const;
                     ^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Location.h:90:22: note: hidden overloaded virtual function 'H5::H5Location::renameAttr' declared here: different number of parameters (2 vs 0)
        virtual void renameAttr(const H5std_string& oldname, const H5std_string& newname) const;
                     ^
2 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c repacker.cpp -o repacker.o
In file included from repacker.cpp:1:
In file included from ./beachmat.h:15:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Cpp.h:27:
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Attribute.h:106:13: warning: 'H5::Attribute::iterateAttrs' hides overloaded virtual function [-Woverloaded-virtual]
        int iterateAttrs() { return 0; }
            ^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Location.h:82:21: note: hidden overloaded virtual function 'H5::H5Location::iterateAttrs' declared here: different number of parameters (3 vs 0)
        virtual int iterateAttrs(attr_operator_t user_op, unsigned* idx = NULL, void* op_data = NULL);
                    ^
In file included from repacker.cpp:1:
In file included from ./beachmat.h:15:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Cpp.h:27:
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Attribute.h:109:14: warning: 'H5::Attribute::renameAttr' hides overloaded virtual functions [-Woverloaded-virtual]
        void renameAttr() {}
             ^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Location.h:89:22: note: hidden overloaded virtual function 'H5::H5Location::renameAttr' declared here: different number of parameters (2 vs 0)
        virtual void renameAttr(const char* oldname, const char* newname) const;
                     ^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Location.h:90:22: note: hidden overloaded virtual function 'H5::H5Location::renameAttr' declared here: different number of parameters (2 vs 0)
        virtual void renameAttr(const H5std_string& oldname, const H5std_string& newname) const;
                     ^
2 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c utils.cpp -o utils.o
In file included from utils.cpp:1:
In file included from ./utils.h:4:
In file included from ./beachmat.h:15:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Cpp.h:27:
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Attribute.h:106:13: warning: 'H5::Attribute::iterateAttrs' hides overloaded virtual function [-Woverloaded-virtual]
        int iterateAttrs() { return 0; }
            ^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Location.h:82:21: note: hidden overloaded virtual function 'H5::H5Location::iterateAttrs' declared here: different number of parameters (3 vs 0)
        virtual int iterateAttrs(attr_operator_t user_op, unsigned* idx = NULL, void* op_data = NULL);
                    ^
In file included from utils.cpp:1:
In file included from ./utils.h:4:
In file included from ./beachmat.h:15:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Cpp.h:27:
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Attribute.h:109:14: warning: 'H5::Attribute::renameAttr' hides overloaded virtual functions [-Woverloaded-virtual]
        void renameAttr() {}
             ^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Location.h:89:22: note: hidden overloaded virtual function 'H5::H5Location::renameAttr' declared here: different number of parameters (2 vs 0)
        virtual void renameAttr(const char* oldname, const char* newname) const;
                     ^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Location.h:90:22: note: hidden overloaded virtual function 'H5::H5Location::renameAttr' declared here: different number of parameters (2 vs 0)
        virtual void renameAttr(const H5std_string& oldname, const H5std_string& newname) const;
                     ^
2 warnings generated.
clang++ -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o beachmat.so 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 /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/lib/libhdf5_cpp.a /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/lib/libhdf5.a /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/lib/libsz.a -lz -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
ar rc 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
clang++ -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o libbeachmat.so 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 `echo 'Rhdf5lib::pkgconfig("PKG_CXX_LIBS")'| "/Library/Frameworks/R.framework/Resources/bin/R" --vanilla --slave` 
mkdir -p "/Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/lib" "/Library/Frameworks/R.framework/Versions/3.5/Resources/library/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   "/Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat"
mv libbeachmat.* "/Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/lib"
installing to /Library/Frameworks/R.framework/Versions/3.5/Resources/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 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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 ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/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 ‘/private/tmp/RtmpaLwXZ7/beachtest.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* 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 for sufficient/correct file permissions ... OK
* checking serialization versions ... OK
* checking whether package ‘beachtest’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
* 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
* 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 ... OK
* checking examples ... NONE
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [93s/95s]
 OK
* DONE

Status: 1 WARNING, 2 NOTEs
See
  ‘/private/tmp/RtmpaLwXZ7/beachtest.Rcheck/00check.log’
for details.


══ testthat results  ═══════════════════════════════════════════════════════════
OK: 109 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
198.407  10.865 215.174 

name	user	system	elapsed
getBestChunkDims	0.002	0.001	0.002
pkgconfig	0.005	0.001	0.006
rechunkByMargins	0.316	0.020	0.342