Package: beachmat

Version: 1.2.1

Command: rm -rf beachmat.buildbin-libdir && mkdir beachmat.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh beachmat_1.2.1.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R beachmat.buildbin-libdir

StartedAt: 2018-10-17 00:57:07 -0400 (Wed, 17 Oct 2018)

EndedAt: 2018-10-17 00:58:59 -0400 (Wed, 17 Oct 2018)

EllapsedTime: 111.8 seconds

RetCode: 0

Status:  OK

PackageFile: beachmat_1.2.1.tgz

PackageFileSize: 6.808 MiB

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###
### Running command:
###
###   rm -rf beachmat.buildbin-libdir && mkdir beachmat.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh beachmat_1.2.1.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R beachmat.buildbin-libdir
###
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>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=beachmat.buildbin-libdir beachmat_1.2.1.tar.gz'
>>>>>>> 

* installing *source* package ‘beachmat’ ...
** libs
rm -f libbeachmat.*
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 "/Users/biocbuild/bbs-3.7-bioc/meat/beachmat.buildbin-libdir/beachmat/lib" "/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   "/Users/biocbuild/bbs-3.7-bioc/meat/beachmat.buildbin-libdir/beachmat/include/beachmat"
mv libbeachmat.* "/Users/biocbuild/bbs-3.7-bioc/meat/beachmat.buildbin-libdir/beachmat/lib"
installing to /Users/biocbuild/bbs-3.7-bioc/meat/beachmat.buildbin-libdir/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)


>>>>>>> 
>>>>>>> FIXING LINKS FOR beachmat.buildbin-libdir/beachmat/libs//beachmat.so
>>>>>>> 

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libgcc_s.1.dylib" "beachmat.buildbin-libdir/beachmat/libs//beachmat.so"
install_name_tool -change "/usr/local/lib/libgfortran.3.dylib" "/Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libgfortran.3.dylib" "beachmat.buildbin-libdir/beachmat/libs//beachmat.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libreadline.5.2.dylib" "beachmat.buildbin-libdir/beachmat/libs//beachmat.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libreadline.dylib" "beachmat.buildbin-libdir/beachmat/libs//beachmat.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libquadmath.0.dylib" "beachmat.buildbin-libdir/beachmat/libs//beachmat.so"