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CHECK report for scran on merida2

This page was generated on 2018-10-17 08:56:23 -0400 (Wed, 17 Oct 2018).

Package 1333/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
scran 1.8.4
Aaron Lun
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/scran
Branch: RELEASE_3_7
Last Commit: bbf1d09
Last Changed Date: 2018-08-07 15:31:02 -0400 (Tue, 07 Aug 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository

Summary

Package: scran
Version: 1.8.4
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:scran.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings scran_1.8.4.tar.gz
StartedAt: 2018-10-16 23:58:10 -0400 (Tue, 16 Oct 2018)
EndedAt: 2018-10-17 00:05:17 -0400 (Wed, 17 Oct 2018)
EllapsedTime: 427.2 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: scran.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:scran.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings scran_1.8.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/scran.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘scran/DESCRIPTION’ ... OK
* this is package ‘scran’ version ‘1.8.4’
* 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 ... NOTE
  installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
File ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/scran/libs/scran.so’:
  Found ‘__ZNSt3__14cerrE’, possibly from ‘std::cerr’ (C++)
  Found ‘___stderrp’, possibly from ‘stderr’ (C)
  Found ‘___stdoutp’, possibly from ‘stdout’ (C)
  Found ‘_abort’, possibly from ‘abort’ (C)
  Found ‘_exit’, possibly from ‘exit’ (C)
  Found ‘_rand_r’, possibly from ‘rand_r’ (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking files in ‘vignettes’ ... OK
* checking examples ... WARNING
Found the following significant warnings:

  Warning: 'exploreData' is deprecated.
  Warning: 'selectorPlot' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
* 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: 1 WARNING, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.7-bioc/meat/scran.Rcheck/00check.log’
for details.

Installation output

scran.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL scran
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘scran’ ...
** libs
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c 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/3.5/Resources/library/beachmat/include/beachmat/integer_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/LIN_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/Input_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/beachmat.h:15:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Cpp.h:27:
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Attribute.h:106:13: warning: 'H5::Attribute::iterateAttrs' hides overloaded virtual function [-Woverloaded-virtual]
        int iterateAttrs() { return 0; }
            ^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Location.h:82:21: note: hidden overloaded virtual function 'H5::H5Location::iterateAttrs' declared here: different number of parameters (3 vs 0)
        virtual int iterateAttrs(attr_operator_t user_op, unsigned* idx = NULL, void* op_data = NULL);
                    ^
In file included from build_snn.cpp:1:
In file included from ./scran.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/integer_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/LIN_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/Input_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/beachmat.h:15:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Cpp.h:27:
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Attribute.h:109:14: warning: 'H5::Attribute::renameAttr' hides overloaded virtual functions [-Woverloaded-virtual]
        void renameAttr() {}
             ^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Location.h:89:22: note: hidden overloaded virtual function 'H5::H5Location::renameAttr' declared here: different number of parameters (2 vs 0)
        virtual void renameAttr(const char* oldname, const char* newname) const;
                     ^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Location.h:90:22: note: hidden overloaded virtual function 'H5::H5Location::renameAttr' declared here: different number of parameters (2 vs 0)
        virtual void renameAttr(const H5std_string& oldname, const H5std_string& newname) const;
                     ^
2 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c calc_log_count_stats.cpp -o calc_log_count_stats.o
In file included from calc_log_count_stats.cpp:1:
In file included from ./scran.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/integer_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/LIN_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/Input_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/beachmat.h:15:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Cpp.h:27:
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Attribute.h:106:13: warning: 'H5::Attribute::iterateAttrs' hides overloaded virtual function [-Woverloaded-virtual]
        int iterateAttrs() { return 0; }
            ^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Location.h:82:21: note: hidden overloaded virtual function 'H5::H5Location::iterateAttrs' declared here: different number of parameters (3 vs 0)
        virtual int iterateAttrs(attr_operator_t user_op, unsigned* idx = NULL, void* op_data = NULL);
                    ^
In file included from calc_log_count_stats.cpp:1:
In file included from ./scran.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/integer_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/LIN_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/Input_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/beachmat.h:15:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Cpp.h:27:
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Attribute.h:109:14: warning: 'H5::Attribute::renameAttr' hides overloaded virtual functions [-Woverloaded-virtual]
        void renameAttr() {}
             ^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Location.h:89:22: note: hidden overloaded virtual function 'H5::H5Location::renameAttr' declared here: different number of parameters (2 vs 0)
        virtual void renameAttr(const char* oldname, const char* newname) const;
                     ^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Location.h:90:22: note: hidden overloaded virtual function 'H5::H5Location::renameAttr' declared here: different number of parameters (2 vs 0)
        virtual void renameAttr(const H5std_string& oldname, const H5std_string& newname) const;
                     ^
2 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c combine_simes.cpp -o combine_simes.o
In file included from combine_simes.cpp:1:
In file included from ./scran.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/integer_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/LIN_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/Input_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/beachmat.h:15:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Cpp.h:27:
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Attribute.h:106:13: warning: 'H5::Attribute::iterateAttrs' hides overloaded virtual function [-Woverloaded-virtual]
        int iterateAttrs() { return 0; }
            ^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Location.h:82:21: note: hidden overloaded virtual function 'H5::H5Location::iterateAttrs' declared here: different number of parameters (3 vs 0)
        virtual int iterateAttrs(attr_operator_t user_op, unsigned* idx = NULL, void* op_data = NULL);
                    ^
In file included from combine_simes.cpp:1:
In file included from ./scran.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/integer_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/LIN_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/Input_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/beachmat.h:15:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Cpp.h:27:
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Attribute.h:109:14: warning: 'H5::Attribute::renameAttr' hides overloaded virtual functions [-Woverloaded-virtual]
        void renameAttr() {}
             ^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Location.h:89:22: note: hidden overloaded virtual function 'H5::H5Location::renameAttr' declared here: different number of parameters (2 vs 0)
        virtual void renameAttr(const char* oldname, const char* newname) const;
                     ^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Location.h:90:22: note: hidden overloaded virtual function 'H5::H5Location::renameAttr' declared here: different number of parameters (2 vs 0)
        virtual void renameAttr(const H5std_string& oldname, const H5std_string& newname) const;
                     ^
2 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c 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/3.5/Resources/library/beachmat/include/beachmat/integer_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/LIN_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/Input_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/beachmat.h:15:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Cpp.h:27:
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Attribute.h:106:13: warning: 'H5::Attribute::iterateAttrs' hides overloaded virtual function [-Woverloaded-virtual]
        int iterateAttrs() { return 0; }
            ^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Location.h:82:21: note: hidden overloaded virtual function 'H5::H5Location::iterateAttrs' declared here: different number of parameters (3 vs 0)
        virtual int iterateAttrs(attr_operator_t user_op, unsigned* idx = NULL, void* op_data = NULL);
                    ^
In file included from compute_CV2.cpp:1:
In file included from ./scran.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/integer_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/LIN_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/Input_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/beachmat.h:15:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Cpp.h:27:
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Attribute.h:109:14: warning: 'H5::Attribute::renameAttr' hides overloaded virtual functions [-Woverloaded-virtual]
        void renameAttr() {}
             ^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Location.h:89:22: note: hidden overloaded virtual function 'H5::H5Location::renameAttr' declared here: different number of parameters (2 vs 0)
        virtual void renameAttr(const char* oldname, const char* newname) const;
                     ^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Location.h:90:22: note: hidden overloaded virtual function 'H5::H5Location::renameAttr' declared here: different number of parameters (2 vs 0)
        virtual void renameAttr(const H5std_string& oldname, const H5std_string& newname) const;
                     ^
2 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c 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/3.5/Resources/library/beachmat/include/beachmat/integer_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/LIN_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/Input_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/beachmat.h:15:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Cpp.h:27:
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Attribute.h:106:13: warning: 'H5::Attribute::iterateAttrs' hides overloaded virtual function [-Woverloaded-virtual]
        int iterateAttrs() { return 0; }
            ^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Location.h:82:21: note: hidden overloaded virtual function 'H5::H5Location::iterateAttrs' declared here: different number of parameters (3 vs 0)
        virtual int iterateAttrs(attr_operator_t user_op, unsigned* idx = NULL, void* op_data = NULL);
                    ^
In file included from compute_rho.cpp:1:
In file included from ./scran.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/integer_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/LIN_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/Input_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/beachmat.h:15:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Cpp.h:27:
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Attribute.h:109:14: warning: 'H5::Attribute::renameAttr' hides overloaded virtual functions [-Woverloaded-virtual]
        void renameAttr() {}
             ^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Location.h:89:22: note: hidden overloaded virtual function 'H5::H5Location::renameAttr' declared here: different number of parameters (2 vs 0)
        virtual void renameAttr(const char* oldname, const char* newname) const;
                     ^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Location.h:90:22: note: hidden overloaded virtual function 'H5::H5Location::renameAttr' declared here: different number of parameters (2 vs 0)
        virtual void renameAttr(const H5std_string& oldname, const H5std_string& newname) const;
                     ^
2 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c find_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/3.5/Resources/library/beachmat/include/beachmat/integer_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/LIN_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/Input_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/beachmat.h:15:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Cpp.h:27:
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Attribute.h:106:13: warning: 'H5::Attribute::iterateAttrs' hides overloaded virtual function [-Woverloaded-virtual]
        int iterateAttrs() { return 0; }
            ^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Location.h:82:21: note: hidden overloaded virtual function 'H5::H5Location::iterateAttrs' declared here: different number of parameters (3 vs 0)
        virtual int iterateAttrs(attr_operator_t user_op, unsigned* idx = NULL, void* op_data = NULL);
                    ^
In file included from find_mutual_nns.cpp:1:
In file included from ./scran.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/integer_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/LIN_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/Input_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/beachmat.h:15:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Cpp.h:27:
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Attribute.h:109:14: warning: 'H5::Attribute::renameAttr' hides overloaded virtual functions [-Woverloaded-virtual]
        void renameAttr() {}
             ^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Location.h:89:22: note: hidden overloaded virtual function 'H5::H5Location::renameAttr' declared here: different number of parameters (2 vs 0)
        virtual void renameAttr(const char* oldname, const char* newname) const;
                     ^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Location.h:90:22: note: hidden overloaded virtual function 'H5::H5Location::renameAttr' declared here: different number of parameters (2 vs 0)
        virtual void renameAttr(const H5std_string& oldname, const H5std_string& newname) const;
                     ^
2 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c 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/3.5/Resources/library/beachmat/include/beachmat/integer_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/LIN_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/Input_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/beachmat.h:15:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Cpp.h:27:
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Attribute.h:106:13: warning: 'H5::Attribute::iterateAttrs' hides overloaded virtual function [-Woverloaded-virtual]
        int iterateAttrs() { return 0; }
            ^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Location.h:82:21: note: hidden overloaded virtual function 'H5::H5Location::iterateAttrs' declared here: different number of parameters (3 vs 0)
        virtual int iterateAttrs(attr_operator_t user_op, unsigned* idx = NULL, void* op_data = NULL);
                    ^
In file included from fit_linear_model.cpp:1:
In file included from ./scran.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/integer_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/LIN_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/Input_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/beachmat.h:15:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Cpp.h:27:
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Attribute.h:109:14: warning: 'H5::Attribute::renameAttr' hides overloaded virtual functions [-Woverloaded-virtual]
        void renameAttr() {}
             ^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Location.h:89:22: note: hidden overloaded virtual function 'H5::H5Location::renameAttr' declared here: different number of parameters (2 vs 0)
        virtual void renameAttr(const char* oldname, const char* newname) const;
                     ^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Location.h:90:22: note: hidden overloaded virtual function 'H5::H5Location::renameAttr' declared here: different number of parameters (2 vs 0)
        virtual void renameAttr(const H5std_string& oldname, const H5std_string& newname) const;
                     ^
2 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c 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/3.5/Resources/library/beachmat/include/beachmat/integer_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/LIN_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/Input_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/beachmat.h:15:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Cpp.h:27:
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Attribute.h:106:13: warning: 'H5::Attribute::iterateAttrs' hides overloaded virtual function [-Woverloaded-virtual]
        int iterateAttrs() { return 0; }
            ^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Location.h:82:21: note: hidden overloaded virtual function 'H5::H5Location::iterateAttrs' declared here: different number of parameters (3 vs 0)
        virtual int iterateAttrs(attr_operator_t user_op, unsigned* idx = NULL, void* op_data = NULL);
                    ^
In file included from forge_system.cpp:1:
In file included from ./scran.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/integer_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/LIN_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/Input_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/beachmat.h:15:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Cpp.h:27:
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Attribute.h:109:14: warning: 'H5::Attribute::renameAttr' hides overloaded virtual functions [-Woverloaded-virtual]
        void renameAttr() {}
             ^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Location.h:89:22: note: hidden overloaded virtual function 'H5::H5Location::renameAttr' declared here: different number of parameters (2 vs 0)
        virtual void renameAttr(const char* oldname, const char* newname) const;
                     ^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Location.h:90:22: note: hidden overloaded virtual function 'H5::H5Location::renameAttr' declared here: different number of parameters (2 vs 0)
        virtual void renameAttr(const H5std_string& oldname, const H5std_string& newname) const;
                     ^
2 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c 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/3.5/Resources/library/beachmat/include/beachmat/integer_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/LIN_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/Input_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/beachmat.h:15:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Cpp.h:27:
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Attribute.h:106:13: warning: 'H5::Attribute::iterateAttrs' hides overloaded virtual function [-Woverloaded-virtual]
        int iterateAttrs() { return 0; }
            ^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Location.h:82:21: note: hidden overloaded virtual function 'H5::H5Location::iterateAttrs' declared here: different number of parameters (3 vs 0)
        virtual int iterateAttrs(attr_operator_t user_op, unsigned* idx = NULL, void* op_data = NULL);
                    ^
In file included from get_residuals.cpp:1:
In file included from ./scran.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/integer_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/LIN_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/Input_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/beachmat.h:15:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Cpp.h:27:
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Attribute.h:109:14: warning: 'H5::Attribute::renameAttr' hides overloaded virtual functions [-Woverloaded-virtual]
        void renameAttr() {}
             ^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Location.h:89:22: note: hidden overloaded virtual function 'H5::H5Location::renameAttr' declared here: different number of parameters (2 vs 0)
        virtual void renameAttr(const char* oldname, const char* newname) const;
                     ^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Location.h:90:22: note: hidden overloaded virtual function 'H5::H5Location::renameAttr' declared here: different number of parameters (2 vs 0)
        virtual void renameAttr(const H5std_string& oldname, const H5std_string& newname) const;
                     ^
2 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c 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/3.5/Resources/library/beachmat/include/beachmat/integer_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/LIN_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/Input_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/beachmat.h:15:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Cpp.h:27:
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Attribute.h:106:13: warning: 'H5::Attribute::iterateAttrs' hides overloaded virtual function [-Woverloaded-virtual]
        int iterateAttrs() { return 0; }
            ^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Location.h:82:21: note: hidden overloaded virtual function 'H5::H5Location::iterateAttrs' declared here: different number of parameters (3 vs 0)
        virtual int iterateAttrs(attr_operator_t user_op, unsigned* idx = NULL, void* op_data = NULL);
                    ^
In file included from get_scaled_ranks.cpp:1:
In file included from ./scran.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/integer_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/LIN_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/Input_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/beachmat.h:15:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Cpp.h:27:
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Attribute.h:109:14: warning: 'H5::Attribute::renameAttr' hides overloaded virtual functions [-Woverloaded-virtual]
        void renameAttr() {}
             ^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Location.h:89:22: note: hidden overloaded virtual function 'H5::H5Location::renameAttr' declared here: different number of parameters (2 vs 0)
        virtual void renameAttr(const char* oldname, const char* newname) const;
                     ^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Location.h:90:22: note: hidden overloaded virtual function 'H5::H5Location::renameAttr' declared here: different number of parameters (2 vs 0)
        virtual void renameAttr(const H5std_string& oldname, const H5std_string& newname) const;
                     ^
2 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c 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/3.5/Resources/library/beachmat/include/beachmat/integer_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/LIN_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/Input_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/beachmat.h:15:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Cpp.h:27:
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Attribute.h:106:13: warning: 'H5::Attribute::iterateAttrs' hides overloaded virtual function [-Woverloaded-virtual]
        int iterateAttrs() { return 0; }
            ^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Location.h:82:21: note: hidden overloaded virtual function 'H5::H5Location::iterateAttrs' declared here: different number of parameters (3 vs 0)
        virtual int iterateAttrs(attr_operator_t user_op, unsigned* idx = NULL, void* op_data = NULL);
                    ^
In file included from init.cpp:1:
In file included from ./scran.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/integer_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/LIN_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/Input_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/beachmat.h:15:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Cpp.h:27:
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Attribute.h:109:14: warning: 'H5::Attribute::renameAttr' hides overloaded virtual functions [-Woverloaded-virtual]
        void renameAttr() {}
             ^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Location.h:89:22: note: hidden overloaded virtual function 'H5::H5Location::renameAttr' declared here: different number of parameters (2 vs 0)
        virtual void renameAttr(const char* oldname, const char* newname) const;
                     ^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Location.h:90:22: note: hidden overloaded virtual function 'H5::H5Location::renameAttr' declared here: different number of parameters (2 vs 0)
        virtual void renameAttr(const H5std_string& oldname, const H5std_string& newname) const;
                     ^
2 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c 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/3.5/Resources/library/beachmat/include/beachmat/integer_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/LIN_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/Input_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/beachmat.h:15:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Cpp.h:27:
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Attribute.h:106:13: warning: 'H5::Attribute::iterateAttrs' hides overloaded virtual function [-Woverloaded-virtual]
        int iterateAttrs() { return 0; }
            ^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Location.h:82:21: note: hidden overloaded virtual function 'H5::H5Location::iterateAttrs' declared here: different number of parameters (3 vs 0)
        virtual int iterateAttrs(attr_operator_t user_op, unsigned* idx = NULL, void* op_data = NULL);
                    ^
In file included from overlap_exprs.cpp:1:
In file included from ./scran.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/integer_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/LIN_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/Input_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/beachmat.h:15:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Cpp.h:27:
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Attribute.h:109:14: warning: 'H5::Attribute::renameAttr' hides overloaded virtual functions [-Woverloaded-virtual]
        void renameAttr() {}
             ^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Location.h:89:22: note: hidden overloaded virtual function 'H5::H5Location::renameAttr' declared here: different number of parameters (2 vs 0)
        virtual void renameAttr(const char* oldname, const char* newname) const;
                     ^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Location.h:90:22: note: hidden overloaded virtual function 'H5::H5Location::renameAttr' declared here: different number of parameters (2 vs 0)
        virtual void renameAttr(const H5std_string& oldname, const H5std_string& newname) const;
                     ^
2 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c 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/3.5/Resources/library/beachmat/include/beachmat/integer_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/LIN_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/Input_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/beachmat.h:15:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Cpp.h:27:
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Attribute.h:106:13: warning: 'H5::Attribute::iterateAttrs' hides overloaded virtual function [-Woverloaded-virtual]
        int iterateAttrs() { return 0; }
            ^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Location.h:82:21: note: hidden overloaded virtual function 'H5::H5Location::iterateAttrs' declared here: different number of parameters (3 vs 0)
        virtual int iterateAttrs(attr_operator_t user_op, unsigned* idx = NULL, void* op_data = NULL);
                    ^
In file included from 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/3.5/Resources/library/beachmat/include/beachmat/integer_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/LIN_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/Input_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/beachmat.h:15:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Cpp.h:27:
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Attribute.h:109:14: warning: 'H5::Attribute::renameAttr' hides overloaded virtual functions [-Woverloaded-virtual]
        void renameAttr() {}
             ^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Location.h:89:22: note: hidden overloaded virtual function 'H5::H5Location::renameAttr' declared here: different number of parameters (2 vs 0)
        virtual void renameAttr(const char* oldname, const char* newname) const;
                     ^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Location.h:90:22: note: hidden overloaded virtual function 'H5::H5Location::renameAttr' declared here: different number of parameters (2 vs 0)
        virtual void renameAttr(const H5std_string& oldname, const H5std_string& newname) const;
                     ^
2 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c shuffle_matrix.cpp -o shuffle_matrix.o
In file included from shuffle_matrix.cpp:1:
In file included from ./scran.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/integer_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/LIN_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/Input_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/beachmat.h:15:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Cpp.h:27:
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Attribute.h:106:13: warning: 'H5::Attribute::iterateAttrs' hides overloaded virtual function [-Woverloaded-virtual]
        int iterateAttrs() { return 0; }
            ^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Location.h:82:21: note: hidden overloaded virtual function 'H5::H5Location::iterateAttrs' declared here: different number of parameters (3 vs 0)
        virtual int iterateAttrs(attr_operator_t user_op, unsigned* idx = NULL, void* op_data = NULL);
                    ^
In file included from shuffle_matrix.cpp:1:
In file included from ./scran.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/integer_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/LIN_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/Input_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/beachmat.h:15:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Cpp.h:27:
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Attribute.h:109:14: warning: 'H5::Attribute::renameAttr' hides overloaded virtual functions [-Woverloaded-virtual]
        void renameAttr() {}
             ^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Location.h:89:22: note: hidden overloaded virtual function 'H5::H5Location::renameAttr' declared here: different number of parameters (2 vs 0)
        virtual void renameAttr(const char* oldname, const char* newname) const;
                     ^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Location.h:90:22: note: hidden overloaded virtual function 'H5::H5Location::renameAttr' declared here: different number of parameters (2 vs 0)
        virtual void renameAttr(const H5std_string& oldname, const H5std_string& newname) const;
                     ^
2 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c 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/3.5/Resources/library/beachmat/include/beachmat/integer_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/LIN_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/Input_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/beachmat.h:15:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Cpp.h:27:
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Attribute.h:106:13: warning: 'H5::Attribute::iterateAttrs' hides overloaded virtual function [-Woverloaded-virtual]
        int iterateAttrs() { return 0; }
            ^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Location.h:82:21: note: hidden overloaded virtual function 'H5::H5Location::iterateAttrs' declared here: different number of parameters (3 vs 0)
        virtual int iterateAttrs(attr_operator_t user_op, unsigned* idx = NULL, void* op_data = NULL);
                    ^
In file included from shuffle_scores.cpp:1:
In file included from ./scran.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/integer_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/LIN_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/Input_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/beachmat.h:15:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Cpp.h:27:
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Attribute.h:109:14: warning: 'H5::Attribute::renameAttr' hides overloaded virtual functions [-Woverloaded-virtual]
        void renameAttr() {}
             ^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Location.h:89:22: note: hidden overloaded virtual function 'H5::H5Location::renameAttr' declared here: different number of parameters (2 vs 0)
        virtual void renameAttr(const char* oldname, const char* newname) const;
                     ^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Location.h:90:22: note: hidden overloaded virtual function 'H5::H5Location::renameAttr' declared here: different number of parameters (2 vs 0)
        virtual void renameAttr(const H5std_string& oldname, const H5std_string& newname) const;
                     ^
2 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c utils.cpp -o utils.o
In file included from utils.cpp:1:
In file included from ./scran.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/integer_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/LIN_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/Input_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/beachmat.h:15:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Cpp.h:27:
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Attribute.h:106:13: warning: 'H5::Attribute::iterateAttrs' hides overloaded virtual function [-Woverloaded-virtual]
        int iterateAttrs() { return 0; }
            ^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Location.h:82:21: note: hidden overloaded virtual function 'H5::H5Location::iterateAttrs' declared here: different number of parameters (3 vs 0)
        virtual int iterateAttrs(attr_operator_t user_op, unsigned* idx = NULL, void* op_data = NULL);
                    ^
In file included from utils.cpp:1:
In file included from ./scran.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/integer_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/LIN_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/Input_matrix.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include/beachmat/beachmat.h:15:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Cpp.h:27:
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Attribute.h:109:14: warning: 'H5::Attribute::renameAttr' hides overloaded virtual functions [-Woverloaded-virtual]
        void renameAttr() {}
             ^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Location.h:89:22: note: hidden overloaded virtual function 'H5::H5Location::renameAttr' declared here: different number of parameters (2 vs 0)
        virtual void renameAttr(const char* oldname, const char* newname) const;
                     ^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include/H5Location.h:90:22: note: hidden overloaded virtual function 'H5::H5Location::renameAttr' declared here: different number of parameters (2 vs 0)
        virtual void renameAttr(const H5std_string& oldname, const H5std_string& newname) const;
                     ^
2 warnings generated.
clang++ -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o scran.so build_snn.o calc_log_count_stats.o combine_simes.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_matrix.o shuffle_scores.o utils.o /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/lib/libbeachmat.a /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/lib/libhdf5_cpp.a /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/lib/libhdf5.a /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/lib/libsz.a -lz -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 /Library/Frameworks/R.framework/Versions/3.5/Resources/library/scran/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (scran)

Tests output

scran.Rcheck/tests/testthat.Rout


R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(scran)
Loading required package: BiocParallel
Loading required package: SingleCellExperiment
Loading required package: SummarizedExperiment
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: DelayedArray
Loading required package: matrixStats

Attaching package: 'matrixStats'

The following objects are masked from 'package:Biobase':

    anyMissing, rowMedians


Attaching package: 'DelayedArray'

The following objects are masked from 'package:matrixStats':

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

The following objects are masked from 'package:base':

    aperm, apply

> test_check("scran")
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 6462 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
197.438   9.117 208.441

Example timings

scran.Rcheck/scran-Ex.timings

nameusersystemelapsed
DM0.1420.0040.147
buildSNNGraph0.1170.0050.126
clusterModularity0.8280.0110.849
combineVar1.9650.0512.033
computeSpikeFactors0.3320.0040.337
computeSumFactors2.3430.0362.396
convertTo3.8450.1554.039
correlatePairs0.2130.0060.220
cyclone0.3870.0080.402
decomposeVar1.1920.0571.258
denoisePCA0.0460.0030.049
exploreData0.3030.0080.315
findMarkers1.0020.0291.038
improvedCV20.3640.0310.396
makeTechTrend0.0330.0020.036
mnnCorrect0.0400.0020.042
multiBlockVar0.9690.0311.008
overlapExprs0.3350.0090.345
parallelPCA0.4090.0910.501
quickCluster0.6920.0160.712
sandbag0.1630.0020.165
selectorPlot0.1700.0020.173
technicalCV20.4520.0480.513
testVar0.0450.0040.052
trendVar0.8890.0520.967