Package: scran

Version: 1.6.9

Command: rm -rf scran.buildbin-libdir && mkdir scran.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh scran_1.6.9.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R scran.buildbin-libdir

StartedAt: 2018-04-12 12:14:02 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 12:15:57 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 114.7 seconds

RetCode: 0

Status:  OK

PackageFile: scran_1.6.9.tgz

PackageFileSize: 1.983 MiB

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###
### Running command:
###
###   rm -rf scran.buildbin-libdir && mkdir scran.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh scran_1.6.9.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R scran.buildbin-libdir
###
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>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=scran.buildbin-libdir scran_1.6.9.tar.gz'
>>>>>>> 

* installing *source* package ‘scran’ ...
** libs
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/beachmat/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rhdf5lib/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c build_snn.cpp -o build_snn.o
In file included from build_snn.cpp:1:
In file included from ./scran.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/beachmat/include/beachmat/integer_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/beachmat/include/beachmat/LIN_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/beachmat/include/beachmat/Input_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/beachmat/include/beachmat/beachmat.h:17:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rhdf5lib/include/c++/H5Cpp.h:27:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rhdf5lib/include/c++/H5Attribute.h:106:13: warning: 'H5::Attribute::iterateAttrs' hides overloaded virtual function [-Woverloaded-virtual]
        int iterateAttrs() { return 0; }
            ^
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rhdf5lib/include/c++/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 build_snn.cpp:1:
In file included from ./scran.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/beachmat/include/beachmat/integer_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/beachmat/include/beachmat/LIN_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/beachmat/include/beachmat/Input_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/beachmat/include/beachmat/beachmat.h:17:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rhdf5lib/include/c++/H5Cpp.h:27:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rhdf5lib/include/c++/H5Attribute.h:109:14: warning: 'H5::Attribute::renameAttr' hides overloaded virtual functions [-Woverloaded-virtual]
        void renameAttr() {}
             ^
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rhdf5lib/include/c++/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/3.4/Resources/library/Rhdf5lib/include/c++/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/3.4/Resources/library/beachmat/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rhdf5lib/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c compute_CV2.cpp -o compute_CV2.o
In file included from compute_CV2.cpp:1:
In file included from ./scran.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/beachmat/include/beachmat/integer_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/beachmat/include/beachmat/LIN_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/beachmat/include/beachmat/Input_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/beachmat/include/beachmat/beachmat.h:17:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rhdf5lib/include/c++/H5Cpp.h:27:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rhdf5lib/include/c++/H5Attribute.h:106:13: warning: 'H5::Attribute::iterateAttrs' hides overloaded virtual function [-Woverloaded-virtual]
        int iterateAttrs() { return 0; }
            ^
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rhdf5lib/include/c++/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 compute_CV2.cpp:1:
In file included from ./scran.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/beachmat/include/beachmat/integer_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/beachmat/include/beachmat/LIN_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/beachmat/include/beachmat/Input_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/beachmat/include/beachmat/beachmat.h:17:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rhdf5lib/include/c++/H5Cpp.h:27:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rhdf5lib/include/c++/H5Attribute.h:109:14: warning: 'H5::Attribute::renameAttr' hides overloaded virtual functions [-Woverloaded-virtual]
        void renameAttr() {}
             ^
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rhdf5lib/include/c++/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/3.4/Resources/library/Rhdf5lib/include/c++/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/3.4/Resources/library/beachmat/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rhdf5lib/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c compute_rho.cpp -o compute_rho.o
In file included from compute_rho.cpp:1:
In file included from ./scran.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/beachmat/include/beachmat/integer_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/beachmat/include/beachmat/LIN_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/beachmat/include/beachmat/Input_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/beachmat/include/beachmat/beachmat.h:17:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rhdf5lib/include/c++/H5Cpp.h:27:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rhdf5lib/include/c++/H5Attribute.h:106:13: warning: 'H5::Attribute::iterateAttrs' hides overloaded virtual function [-Woverloaded-virtual]
        int iterateAttrs() { return 0; }
            ^
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rhdf5lib/include/c++/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 compute_rho.cpp:1:
In file included from ./scran.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/beachmat/include/beachmat/integer_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/beachmat/include/beachmat/LIN_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/beachmat/include/beachmat/Input_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/beachmat/include/beachmat/beachmat.h:17:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rhdf5lib/include/c++/H5Cpp.h:27:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rhdf5lib/include/c++/H5Attribute.h:109:14: warning: 'H5::Attribute::renameAttr' hides overloaded virtual functions [-Woverloaded-virtual]
        void renameAttr() {}
             ^
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rhdf5lib/include/c++/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/3.4/Resources/library/Rhdf5lib/include/c++/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/3.4/Resources/library/beachmat/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rhdf5lib/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c find_mutual_nns.cpp -o find_mutual_nns.o
In file included from find_mutual_nns.cpp:1:
In file included from ./scran.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/beachmat/include/beachmat/integer_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/beachmat/include/beachmat/LIN_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/beachmat/include/beachmat/Input_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/beachmat/include/beachmat/beachmat.h:17:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rhdf5lib/include/c++/H5Cpp.h:27:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rhdf5lib/include/c++/H5Attribute.h:106:13: warning: 'H5::Attribute::iterateAttrs' hides overloaded virtual function [-Woverloaded-virtual]
        int iterateAttrs() { return 0; }
            ^
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rhdf5lib/include/c++/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_mutual_nns.cpp:1:
In file included from ./scran.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/beachmat/include/beachmat/integer_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/beachmat/include/beachmat/LIN_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/beachmat/include/beachmat/Input_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/beachmat/include/beachmat/beachmat.h:17:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rhdf5lib/include/c++/H5Cpp.h:27:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rhdf5lib/include/c++/H5Attribute.h:109:14: warning: 'H5::Attribute::renameAttr' hides overloaded virtual functions [-Woverloaded-virtual]
        void renameAttr() {}
             ^
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rhdf5lib/include/c++/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/3.4/Resources/library/Rhdf5lib/include/c++/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/3.4/Resources/library/beachmat/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rhdf5lib/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c fit_linear_model.cpp -o fit_linear_model.o
In file included from fit_linear_model.cpp:1:
In file included from ./scran.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/beachmat/include/beachmat/integer_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/beachmat/include/beachmat/LIN_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/beachmat/include/beachmat/Input_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/beachmat/include/beachmat/beachmat.h:17:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rhdf5lib/include/c++/H5Cpp.h:27:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rhdf5lib/include/c++/H5Attribute.h:106:13: warning: 'H5::Attribute::iterateAttrs' hides overloaded virtual function [-Woverloaded-virtual]
        int iterateAttrs() { return 0; }
            ^
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rhdf5lib/include/c++/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 fit_linear_model.cpp:1:
In file included from ./scran.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/beachmat/include/beachmat/integer_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/beachmat/include/beachmat/LIN_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/beachmat/include/beachmat/Input_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/beachmat/include/beachmat/beachmat.h:17:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rhdf5lib/include/c++/H5Cpp.h:27:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rhdf5lib/include/c++/H5Attribute.h:109:14: warning: 'H5::Attribute::renameAttr' hides overloaded virtual functions [-Woverloaded-virtual]
        void renameAttr() {}
             ^
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rhdf5lib/include/c++/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/3.4/Resources/library/Rhdf5lib/include/c++/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/3.4/Resources/library/beachmat/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rhdf5lib/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c forge_system.cpp -o forge_system.o
In file included from forge_system.cpp:1:
In file included from ./scran.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/beachmat/include/beachmat/integer_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/beachmat/include/beachmat/LIN_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/beachmat/include/beachmat/Input_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/beachmat/include/beachmat/beachmat.h:17:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rhdf5lib/include/c++/H5Cpp.h:27:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rhdf5lib/include/c++/H5Attribute.h:106:13: warning: 'H5::Attribute::iterateAttrs' hides overloaded virtual function [-Woverloaded-virtual]
        int iterateAttrs() { return 0; }
            ^
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rhdf5lib/include/c++/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 forge_system.cpp:1:
In file included from ./scran.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/beachmat/include/beachmat/integer_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/beachmat/include/beachmat/LIN_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/beachmat/include/beachmat/Input_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/beachmat/include/beachmat/beachmat.h:17:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rhdf5lib/include/c++/H5Cpp.h:27:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rhdf5lib/include/c++/H5Attribute.h:109:14: warning: 'H5::Attribute::renameAttr' hides overloaded virtual functions [-Woverloaded-virtual]
        void renameAttr() {}
             ^
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rhdf5lib/include/c++/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/3.4/Resources/library/Rhdf5lib/include/c++/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/3.4/Resources/library/beachmat/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rhdf5lib/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c get_residuals.cpp -o get_residuals.o
In file included from get_residuals.cpp:1:
In file included from ./scran.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/beachmat/include/beachmat/integer_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/beachmat/include/beachmat/LIN_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/beachmat/include/beachmat/Input_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/beachmat/include/beachmat/beachmat.h:17:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rhdf5lib/include/c++/H5Cpp.h:27:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rhdf5lib/include/c++/H5Attribute.h:106:13: warning: 'H5::Attribute::iterateAttrs' hides overloaded virtual function [-Woverloaded-virtual]
        int iterateAttrs() { return 0; }
            ^
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rhdf5lib/include/c++/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 get_residuals.cpp:1:
In file included from ./scran.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/beachmat/include/beachmat/integer_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/beachmat/include/beachmat/LIN_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/beachmat/include/beachmat/Input_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/beachmat/include/beachmat/beachmat.h:17:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rhdf5lib/include/c++/H5Cpp.h:27:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rhdf5lib/include/c++/H5Attribute.h:109:14: warning: 'H5::Attribute::renameAttr' hides overloaded virtual functions [-Woverloaded-virtual]
        void renameAttr() {}
             ^
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rhdf5lib/include/c++/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/3.4/Resources/library/Rhdf5lib/include/c++/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/3.4/Resources/library/beachmat/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rhdf5lib/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c get_scaled_ranks.cpp -o get_scaled_ranks.o
In file included from get_scaled_ranks.cpp:1:
In file included from ./scran.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/beachmat/include/beachmat/integer_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/beachmat/include/beachmat/LIN_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/beachmat/include/beachmat/Input_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/beachmat/include/beachmat/beachmat.h:17:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rhdf5lib/include/c++/H5Cpp.h:27:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rhdf5lib/include/c++/H5Attribute.h:106:13: warning: 'H5::Attribute::iterateAttrs' hides overloaded virtual function [-Woverloaded-virtual]
        int iterateAttrs() { return 0; }
            ^
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rhdf5lib/include/c++/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 get_scaled_ranks.cpp:1:
In file included from ./scran.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/beachmat/include/beachmat/integer_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/beachmat/include/beachmat/LIN_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/beachmat/include/beachmat/Input_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/beachmat/include/beachmat/beachmat.h:17:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rhdf5lib/include/c++/H5Cpp.h:27:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rhdf5lib/include/c++/H5Attribute.h:109:14: warning: 'H5::Attribute::renameAttr' hides overloaded virtual functions [-Woverloaded-virtual]
        void renameAttr() {}
             ^
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rhdf5lib/include/c++/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/3.4/Resources/library/Rhdf5lib/include/c++/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/3.4/Resources/library/beachmat/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rhdf5lib/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c init.cpp -o init.o
In file included from init.cpp:1:
In file included from ./scran.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/beachmat/include/beachmat/integer_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/beachmat/include/beachmat/LIN_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/beachmat/include/beachmat/Input_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/beachmat/include/beachmat/beachmat.h:17:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rhdf5lib/include/c++/H5Cpp.h:27:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rhdf5lib/include/c++/H5Attribute.h:106:13: warning: 'H5::Attribute::iterateAttrs' hides overloaded virtual function [-Woverloaded-virtual]
        int iterateAttrs() { return 0; }
            ^
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rhdf5lib/include/c++/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 init.cpp:1:
In file included from ./scran.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/beachmat/include/beachmat/integer_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/beachmat/include/beachmat/LIN_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/beachmat/include/beachmat/Input_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/beachmat/include/beachmat/beachmat.h:17:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rhdf5lib/include/c++/H5Cpp.h:27:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rhdf5lib/include/c++/H5Attribute.h:109:14: warning: 'H5::Attribute::renameAttr' hides overloaded virtual functions [-Woverloaded-virtual]
        void renameAttr() {}
             ^
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rhdf5lib/include/c++/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/3.4/Resources/library/Rhdf5lib/include/c++/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/3.4/Resources/library/beachmat/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rhdf5lib/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c overlap_exprs.cpp -o overlap_exprs.o
In file included from overlap_exprs.cpp:1:
In file included from ./scran.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/beachmat/include/beachmat/integer_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/beachmat/include/beachmat/LIN_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/beachmat/include/beachmat/Input_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/beachmat/include/beachmat/beachmat.h:17:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rhdf5lib/include/c++/H5Cpp.h:27:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rhdf5lib/include/c++/H5Attribute.h:106:13: warning: 'H5::Attribute::iterateAttrs' hides overloaded virtual function [-Woverloaded-virtual]
        int iterateAttrs() { return 0; }
            ^
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rhdf5lib/include/c++/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 overlap_exprs.cpp:1:
In file included from ./scran.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/beachmat/include/beachmat/integer_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/beachmat/include/beachmat/LIN_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/beachmat/include/beachmat/Input_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/beachmat/include/beachmat/beachmat.h:17:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rhdf5lib/include/c++/H5Cpp.h:27:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rhdf5lib/include/c++/H5Attribute.h:109:14: warning: 'H5::Attribute::renameAttr' hides overloaded virtual functions [-Woverloaded-virtual]
        void renameAttr() {}
             ^
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rhdf5lib/include/c++/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/3.4/Resources/library/Rhdf5lib/include/c++/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/3.4/Resources/library/beachmat/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rhdf5lib/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c run_dormqr.cpp -o run_dormqr.o
In file included from run_dormqr.cpp:1:
In file included from ./run_dormqr.h:4:
In file included from ./scran.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/beachmat/include/beachmat/integer_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/beachmat/include/beachmat/LIN_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/beachmat/include/beachmat/Input_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/beachmat/include/beachmat/beachmat.h:17:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rhdf5lib/include/c++/H5Cpp.h:27:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rhdf5lib/include/c++/H5Attribute.h:106:13: warning: 'H5::Attribute::iterateAttrs' hides overloaded virtual function [-Woverloaded-virtual]
        int iterateAttrs() { return 0; }
            ^
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rhdf5lib/include/c++/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 run_dormqr.cpp:1:
In file included from ./run_dormqr.h:4:
In file included from ./scran.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/beachmat/include/beachmat/integer_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/beachmat/include/beachmat/LIN_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/beachmat/include/beachmat/Input_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/beachmat/include/beachmat/beachmat.h:17:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rhdf5lib/include/c++/H5Cpp.h:27:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rhdf5lib/include/c++/H5Attribute.h:109:14: warning: 'H5::Attribute::renameAttr' hides overloaded virtual functions [-Woverloaded-virtual]
        void renameAttr() {}
             ^
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rhdf5lib/include/c++/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/3.4/Resources/library/Rhdf5lib/include/c++/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/3.4/Resources/library/beachmat/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rhdf5lib/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c shuffle_scores.cpp -o shuffle_scores.o
In file included from shuffle_scores.cpp:1:
In file included from ./scran.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/beachmat/include/beachmat/integer_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/beachmat/include/beachmat/LIN_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/beachmat/include/beachmat/Input_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/beachmat/include/beachmat/beachmat.h:17:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rhdf5lib/include/c++/H5Cpp.h:27:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rhdf5lib/include/c++/H5Attribute.h:106:13: warning: 'H5::Attribute::iterateAttrs' hides overloaded virtual function [-Woverloaded-virtual]
        int iterateAttrs() { return 0; }
            ^
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rhdf5lib/include/c++/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 shuffle_scores.cpp:1:
In file included from ./scran.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/beachmat/include/beachmat/integer_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/beachmat/include/beachmat/LIN_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/beachmat/include/beachmat/Input_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/beachmat/include/beachmat/beachmat.h:17:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rhdf5lib/include/c++/H5Cpp.h:27:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rhdf5lib/include/c++/H5Attribute.h:109:14: warning: 'H5::Attribute::renameAttr' hides overloaded virtual functions [-Woverloaded-virtual]
        void renameAttr() {}
             ^
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rhdf5lib/include/c++/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/3.4/Resources/library/Rhdf5lib/include/c++/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/3.4/Resources/library/beachmat/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rhdf5lib/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c sum_spikes.cpp -o sum_spikes.o
In file included from sum_spikes.cpp:1:
In file included from ./scran.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/beachmat/include/beachmat/integer_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/beachmat/include/beachmat/LIN_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/beachmat/include/beachmat/Input_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/beachmat/include/beachmat/beachmat.h:17:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rhdf5lib/include/c++/H5Cpp.h:27:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rhdf5lib/include/c++/H5Attribute.h:106:13: warning: 'H5::Attribute::iterateAttrs' hides overloaded virtual function [-Woverloaded-virtual]
        int iterateAttrs() { return 0; }
            ^
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rhdf5lib/include/c++/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 sum_spikes.cpp:1:
In file included from ./scran.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/beachmat/include/beachmat/integer_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/beachmat/include/beachmat/LIN_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/beachmat/include/beachmat/Input_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/beachmat/include/beachmat/beachmat.h:17:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rhdf5lib/include/c++/H5Cpp.h:27:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rhdf5lib/include/c++/H5Attribute.h:109:14: warning: 'H5::Attribute::renameAttr' hides overloaded virtual functions [-Woverloaded-virtual]
        void renameAttr() {}
             ^
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rhdf5lib/include/c++/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/3.4/Resources/library/Rhdf5lib/include/c++/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/3.4/Resources/library/beachmat/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/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 ./scran.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/beachmat/include/beachmat/integer_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/beachmat/include/beachmat/LIN_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/beachmat/include/beachmat/Input_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/beachmat/include/beachmat/beachmat.h:17:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rhdf5lib/include/c++/H5Cpp.h:27:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rhdf5lib/include/c++/H5Attribute.h:106:13: warning: 'H5::Attribute::iterateAttrs' hides overloaded virtual function [-Woverloaded-virtual]
        int iterateAttrs() { return 0; }
            ^
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rhdf5lib/include/c++/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 ./scran.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/beachmat/include/beachmat/integer_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/beachmat/include/beachmat/LIN_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/beachmat/include/beachmat/Input_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/beachmat/include/beachmat/beachmat.h:17:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rhdf5lib/include/c++/H5Cpp.h:27:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rhdf5lib/include/c++/H5Attribute.h:109:14: warning: 'H5::Attribute::renameAttr' hides overloaded virtual functions [-Woverloaded-virtual]
        void renameAttr() {}
             ^
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rhdf5lib/include/c++/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/3.4/Resources/library/Rhdf5lib/include/c++/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 scran.so build_snn.o compute_CV2.o compute_rho.o find_mutual_nns.o fit_linear_model.o forge_system.o get_residuals.o get_scaled_ranks.o init.o overlap_exprs.o run_dormqr.o shuffle_scores.o sum_spikes.o utils.o /Library/Frameworks/R.framework/Versions/3.4/Resources/library/beachmat/lib/libbeachmat.a /Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rhdf5lib/lib/libhdf5_cpp.a /Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rhdf5lib/lib/libhdf5.a /Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rhdf5lib/lib/libsz.a -pthread -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
clang-4.0: warning: argument unused during compilation: '-pthread' [-Wunused-command-line-argument]
installing to /Users/biocbuild/bbs-3.6-bioc/meat/scran.buildbin-libdir/scran/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (scran)


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

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libgcc_s.1.dylib" "scran.buildbin-libdir/scran/libs//scran.so"
install_name_tool -change "/usr/local/lib/libgfortran.3.dylib" "/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libgfortran.3.dylib" "scran.buildbin-libdir/scran/libs//scran.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libreadline.5.2.dylib" "scran.buildbin-libdir/scran/libs//scran.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libreadline.dylib" "scran.buildbin-libdir/scran/libs//scran.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libquadmath.0.dylib" "scran.buildbin-libdir/scran/libs//scran.so"
install_name_tool -change "/usr/local/gfortran/lib/libgfortran.3.dylib" "/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libgfortran.3.dylib" "scran.buildbin-libdir/scran/libs//scran.so"
install_name_tool -change "/usr/local/gfortran/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libquadmath.0.dylib" "scran.buildbin-libdir/scran/libs//scran.so"