Package: scran

Version: 1.11.25

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_1.11.25.tar.gz

StartedAt: 2019-04-09 03:37:57 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 03:47:50 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 593.8 seconds

RetCode: 0

Status:  OK

CheckDir: scran.Rcheck

Warnings: 0

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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_1.11.25.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/scran.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* 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 ‘1.11.25’
* 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 ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/scran.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL scran
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/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/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/beachmat/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/dqrng/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c build_snn.cpp -o build_snn.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/beachmat/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/dqrng/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c calc_log_count_stats.cpp -o calc_log_count_stats.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/beachmat/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/dqrng/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c combine_rho.cpp -o combine_rho.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/beachmat/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/dqrng/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c combine_simes.cpp -o combine_simes.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/beachmat/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/dqrng/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c compute_CV2.cpp -o compute_CV2.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/beachmat/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/dqrng/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c compute_rho_null.cpp -o compute_rho_null.o
In file included from compute_rho_null.cpp:4:
In file included from ./rand_custom.h:6:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include/boost/random.hpp:36:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include/boost/random/additive_combine.hpp:27:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include/boost/random/linear_congruential.hpp:30:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include/boost/random/detail/const_mod.hpp:23:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include/boost/random/detail/large_arithmetic.hpp:19:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include/boost/random/detail/integer_log2.hpp:19:
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include/boost/pending/integer_log2.hpp:7:1: warning: This header is deprecated. Use <boost/integer/integer_log2.hpp> instead. [-W#pragma-messages]
BOOST_HEADER_DEPRECATED("<boost/integer/integer_log2.hpp>");
^
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include/boost/config/header_deprecated.hpp:23:37: note: expanded from macro 'BOOST_HEADER_DEPRECATED'
# define BOOST_HEADER_DEPRECATED(a) BOOST_PRAGMA_MESSAGE("This header is deprecated. Use " a " instead.")
                                    ^
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include/boost/config/pragma_message.hpp:24:34: note: expanded from macro 'BOOST_PRAGMA_MESSAGE'
# define BOOST_PRAGMA_MESSAGE(x) _Pragma(BOOST_STRINGIZE(message(x)))
                                 ^
<scratch space>:159:2: note: expanded from here
 message("This header is deprecated. Use " "<boost/integer/integer_log2.hpp>" " instead.")
 ^
1 warning generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/beachmat/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/dqrng/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c compute_rho_pairs.cpp -o compute_rho_pairs.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/beachmat/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/dqrng/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c cyclone_scores.cpp -o cyclone_scores.o
In file included from cyclone_scores.cpp:7:
In file included from ./rand_custom.h:6:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include/boost/random.hpp:36:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include/boost/random/additive_combine.hpp:27:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include/boost/random/linear_congruential.hpp:30:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include/boost/random/detail/const_mod.hpp:23:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include/boost/random/detail/large_arithmetic.hpp:19:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include/boost/random/detail/integer_log2.hpp:19:
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include/boost/pending/integer_log2.hpp:7:1: warning: This header is deprecated. Use <boost/integer/integer_log2.hpp> instead. [-W#pragma-messages]
BOOST_HEADER_DEPRECATED("<boost/integer/integer_log2.hpp>");
^
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include/boost/config/header_deprecated.hpp:23:37: note: expanded from macro 'BOOST_HEADER_DEPRECATED'
# define BOOST_HEADER_DEPRECATED(a) BOOST_PRAGMA_MESSAGE("This header is deprecated. Use " a " instead.")
                                    ^
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include/boost/config/pragma_message.hpp:24:34: note: expanded from macro 'BOOST_PRAGMA_MESSAGE'
# define BOOST_PRAGMA_MESSAGE(x) _Pragma(BOOST_STRINGIZE(message(x)))
                                 ^
<scratch space>:159:2: note: expanded from here
 message("This header is deprecated. Use " "<boost/integer/integer_log2.hpp>" " instead.")
 ^
1 warning generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/beachmat/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/dqrng/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c find_mutual_nns.cpp -o find_mutual_nns.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/beachmat/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/dqrng/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c fit_linear_model.cpp -o fit_linear_model.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/beachmat/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/dqrng/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c get_residuals.cpp -o get_residuals.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/beachmat/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/dqrng/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c get_scaled_ranks.cpp -o get_scaled_ranks.o
get_scaled_ranks.cpp:67:16: warning: unused variable 'accumulated_rank' [-Wunused-variable]
        double accumulated_rank=0;
               ^
1 warning generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/beachmat/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/dqrng/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c init.cpp -o init.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/beachmat/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/dqrng/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c overlap_exprs.cpp -o overlap_exprs.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/beachmat/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/dqrng/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c pool_size_factors.cpp -o pool_size_factors.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/beachmat/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/dqrng/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c rand_custom.cpp -o rand_custom.o
In file included from rand_custom.cpp:1:
In file included from ./rand_custom.h:6:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include/boost/random.hpp:36:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include/boost/random/additive_combine.hpp:27:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include/boost/random/linear_congruential.hpp:30:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include/boost/random/detail/const_mod.hpp:23:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include/boost/random/detail/large_arithmetic.hpp:19:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include/boost/random/detail/integer_log2.hpp:19:
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include/boost/pending/integer_log2.hpp:7:1: warning: This header is deprecated. Use <boost/integer/integer_log2.hpp> instead. [-W#pragma-messages]
BOOST_HEADER_DEPRECATED("<boost/integer/integer_log2.hpp>");
^
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include/boost/config/header_deprecated.hpp:23:37: note: expanded from macro 'BOOST_HEADER_DEPRECATED'
# define BOOST_HEADER_DEPRECATED(a) BOOST_PRAGMA_MESSAGE("This header is deprecated. Use " a " instead.")
                                    ^
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include/boost/config/pragma_message.hpp:24:34: note: expanded from macro 'BOOST_PRAGMA_MESSAGE'
# define BOOST_PRAGMA_MESSAGE(x) _Pragma(BOOST_STRINGIZE(message(x)))
                                 ^
<scratch space>:159:2: note: expanded from here
 message("This header is deprecated. Use " "<boost/integer/integer_log2.hpp>" " instead.")
 ^
1 warning generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/beachmat/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/dqrng/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c run_dormqr.cpp -o run_dormqr.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/beachmat/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/dqrng/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c shuffle_matrix.cpp -o shuffle_matrix.o
In file included from shuffle_matrix.cpp:7:
In file included from ./rand_custom.h:6:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include/boost/random.hpp:36:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include/boost/random/additive_combine.hpp:27:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include/boost/random/linear_congruential.hpp:30:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include/boost/random/detail/const_mod.hpp:23:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include/boost/random/detail/large_arithmetic.hpp:19:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include/boost/random/detail/integer_log2.hpp:19:
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include/boost/pending/integer_log2.hpp:7:1: warning: This header is deprecated. Use <boost/integer/integer_log2.hpp> instead. [-W#pragma-messages]
BOOST_HEADER_DEPRECATED("<boost/integer/integer_log2.hpp>");
^
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include/boost/config/header_deprecated.hpp:23:37: note: expanded from macro 'BOOST_HEADER_DEPRECATED'
# define BOOST_HEADER_DEPRECATED(a) BOOST_PRAGMA_MESSAGE("This header is deprecated. Use " a " instead.")
                                    ^
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include/boost/config/pragma_message.hpp:24:34: note: expanded from macro 'BOOST_PRAGMA_MESSAGE'
# define BOOST_PRAGMA_MESSAGE(x) _Pragma(BOOST_STRINGIZE(message(x)))
                                 ^
<scratch space>:159:2: note: expanded from here
 message("This header is deprecated. Use " "<boost/integer/integer_log2.hpp>" " instead.")
 ^
1 warning generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/beachmat/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/dqrng/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c subset_and_divide.cpp -o subset_and_divide.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/beachmat/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/dqrng/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c test_shuffle.cpp -o test_shuffle.o
In file included from test_shuffle.cpp:3:
In file included from ./rand_custom.h:6:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include/boost/random.hpp:36:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include/boost/random/additive_combine.hpp:27:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include/boost/random/linear_congruential.hpp:30:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include/boost/random/detail/const_mod.hpp:23:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include/boost/random/detail/large_arithmetic.hpp:19:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include/boost/random/detail/integer_log2.hpp:19:
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include/boost/pending/integer_log2.hpp:7:1: warning: This header is deprecated. Use <boost/integer/integer_log2.hpp> instead. [-W#pragma-messages]
BOOST_HEADER_DEPRECATED("<boost/integer/integer_log2.hpp>");
^
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include/boost/config/header_deprecated.hpp:23:37: note: expanded from macro 'BOOST_HEADER_DEPRECATED'
# define BOOST_HEADER_DEPRECATED(a) BOOST_PRAGMA_MESSAGE("This header is deprecated. Use " a " instead.")
                                    ^
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include/boost/config/pragma_message.hpp:24:34: note: expanded from macro 'BOOST_PRAGMA_MESSAGE'
# define BOOST_PRAGMA_MESSAGE(x) _Pragma(BOOST_STRINGIZE(message(x)))
                                 ^
<scratch space>:159:2: note: expanded from here
 message("This header is deprecated. Use " "<boost/integer/integer_log2.hpp>" " instead.")
 ^
1 warning generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/beachmat/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/dqrng/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c utils.cpp -o utils.o
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_rho.o combine_simes.o compute_CV2.o compute_rho_null.o compute_rho_pairs.o cyclone_scores.o find_mutual_nns.o fit_linear_model.o get_residuals.o get_scaled_ranks.o init.o overlap_exprs.o pool_size_factors.o rand_custom.o run_dormqr.o shuffle_matrix.o subset_and_divide.o test_shuffle.o utils.o -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
installing to /Library/Frameworks/R.framework/Versions/3.6/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)

R Under development (unstable) (2018-11-27 r75683) -- "Unsuffered Consequences"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-bit)

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> library(testthat)
> library(scran)
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, 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

Loading required package: BiocParallel

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, rowsum

> test_check("scran")
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 12019 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
329.297  19.312 347.938 

name	user	system	elapsed
DM	0.145	0.026	0.172
buildSNNGraph	0.336	0.038	0.379
cleanSizeFactors	0.029	0.002	0.032
clusterModularity	0.295	0.019	0.359
combineMarkers	1.525	0.032	1.576
combinePValues	0.022	0.006	0.028
combineVar	1.811	0.026	1.850
computeSpikeFactors	0.252	0.001	0.256
computeSumFactors	1.907	0.033	1.950
convertTo	3.941	0.134	4.108
correlateGenes	0.312	0.009	0.324
correlatePairs	0.319	0.011	0.334
cosineNorm	0.006	0.000	0.007
cyclone	0.266	0.007	0.285
decomposeVar	1.706	0.062	1.786
denoisePCA	0.066	0.002	0.070
doubletCells	0.976	0.051	1.036
doubletCluster	0.450	0.004	0.460
fastMNN	0	0	0
findMarkers	1.008	0.013	1.028
improvedCV2	0.394	0.019	0.420
makeTechTrend	0.037	0.002	0.045
mnnCorrect	0	0	0
multiBatchNorm	0	0	0
multiBatchPCA	0.000	0.001	0.000
multiBlockNorm	0.743	0.018	0.768
multiBlockVar	1.691	0.032	1.736
overlapExprs	0.506	0.020	0.534
pairwiseTTests	0.486	0.023	0.511
pairwiseWilcox	1.074	0.011	1.093
parallelPCA	1.658	0.179	1.846
quickCluster	1.476	0.032	1.522
sandbag	0.192	0.002	0.196
scaledColRanks	0.117	0.004	0.122
technicalCV2	0.387	0.039	0.429
testVar	0.046	0.004	0.052
trendVar	0.896	0.029	0.933