BioC 3.6: CHECK report for scran on veracruz1

Package: scran

Version: 1.5.8

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings scran_1.5.8.tar.gz

StartedAt: 2017-08-16 08:20:33 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 08:27:32 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 419.7 seconds

RetCode: 0

Status:  OK

CheckDir: scran.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings scran_1.5.8.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/scran.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘scran/DESCRIPTION’ ... OK
* this is package ‘scran’ version ‘1.5.8’
* 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 ‘scran’ can be installed ... OK
* checking installed package size ... OK
* 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 ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
           user system elapsed
convertTo 5.192  0.105    5.45
* 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: OK

* 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 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 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 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 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.Rcheck/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)

name	user	system	elapsed
DM	0.161	0.004	0.169
buildSNNGraph	0.128	0.003	0.133
combineVar	4.519	0.065	4.743
computeSpikeFactors	1.139	0.010	1.198
computeSumFactors	1.820	0.038	1.906
convertTo	5.192	0.105	5.450
correlatePairs	0.259	0.004	0.270
cyclone	0.396	0.004	0.420
decomposeVar	2.254	0.034	2.363
denoisePCA	0.200	0.014	0.227
exploreData	0.836	0.031	0.912
findMarkers	1.185	0.036	1.251
improvedCV2	1.233	0.047	1.316
mnnCorrect	0.094	0.007	0.103
overlapExprs	1.001	0.021	1.046
quickCluster	1.042	0.023	1.100
sandbag	0.101	0.001	0.102
selectorPlot	0.549	0.007	0.574
spikes	1.050	0.023	1.135
technicalCV2	1.159	0.055	1.266
testVar	0.038	0.004	0.043
trendVar	1.880	0.027	1.970