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CHECK report for scran on tokay1

This page was generated on 2020-04-15 12:26:32 -0400 (Wed, 15 Apr 2020).

Package 1545/1823HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
scran 1.14.6
Aaron Lun
Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/scran
Branch: RELEASE_3_10
Last Commit: 240fad2
Last Changed Date: 2020-01-30 00:15:28 -0400 (Thu, 30 Jan 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: scran
Version: 1.14.6
Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:scran.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings scran_1.14.6.tar.gz
StartedAt: 2020-04-15 06:28:32 -0400 (Wed, 15 Apr 2020)
EndedAt: 2020-04-15 06:45:38 -0400 (Wed, 15 Apr 2020)
EllapsedTime: 1025.8 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: scran.Rcheck
Warnings: 2

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:scran.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings scran_1.14.6.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/scran.Rcheck'
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'scran/DESCRIPTION' ... OK
* this is package 'scran' version '1.14.6'
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.10-bioc/R/library/scran/libs/i386/scran.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)
File 'C:/Users/biocbuild/bbs-3.10-bioc/R/library/scran/libs/x64/scran.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (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 ...
** running examples for arch 'i386' ... WARNING
Found the following significant warnings:

  Warning: handling of spike-ins via 'isSpike()' is deprecated.
  Warning: 'normalizeSCE' is deprecated.
  Warning: 'centreSizeFactors' is deprecated.
  Warning: 'trendVar' is deprecated.
  Warning: 'decomposeVar' is deprecated.
  Warning: 'testVar' is deprecated.
  Warning: 'trendVar' is deprecated.
  Warning: 'decomposeVar' is deprecated.
  Warning: 'testVar' is deprecated.
  Warning: 'normalizeSCE' is deprecated.
  Warning: 'centreSizeFactors' is deprecated.
  Warning: 'clusters=' is deprecated.
  Warning: 'improvedCV2' is deprecated.
  Warning: handling of spike-ins via 'isSpike()' is deprecated.
  Warning: 'multiBlockNorm' is deprecated.
  Warning: 'normalizeSCE' is deprecated.
  Warning: handling of spike-ins via 'isSpike()' is deprecated.
  Warning: 'multiBlockNorm' is deprecated.
  Warning: 'normalizeSCE' is deprecated.
  Warning: 'multiBlockVar' is deprecated.
  Warning: 'type=' is deprecated.
  Warning: 'trendVar' is deprecated.
  Warning: 'decomposeVar' is deprecated.
  Warning: 'testVar' is deprecated.
  Warning: 'type=' is deprecated.
  Warning: 'trendVar' is deprecated.
  Warning: 'decomposeVar' is deprecated.
  Warning: 'testVar' is deprecated.
  Warning: 'type=' is deprecated.
  Warning: 'trendVar' is deprecated.
  Warning: 'decomposeVar' is deprecated.
  Warning: 'testVar' is deprecated.
  Warning: 'isSpike' is deprecated.
  Warning: 'normalizeSCE' is deprecated.
  Warning: 'centreSizeFactors' is deprecated.
  Warning: handling of spike-ins via 'isSpike()' is deprecated.
  Warning: 'overlapExprs' is deprecated.
  Warning: 'parallelPCA' is deprecated.
  Warning: 'technicalCV2' is deprecated.
  Warning: 'isSpike<-' is deprecated.
  Warning: 'spikeNames' is deprecated.
  Warning: 'isSpike' is deprecated.
  Warning: 'technicalCV2' is deprecated.
  Warning: 'testVar' is deprecated.
  Warning: 'testVar' is deprecated.
  Warning: 'testVar' is deprecated.
  Warning: handling of spike-ins via 'isSpike()' is deprecated.
  Warning: 'normalizeSCE' is deprecated.
  Warning: 'centreSizeFactors' is deprecated.
  Warning: 'trendVar' is deprecated.
  Warning: 'trendVar' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Examples with CPU or elapsed time > 5s
                   user system elapsed
cyclone           20.23   0.75   21.00
bootstrapCluster  14.46   0.52   15.14
buildSNNGraph      7.99   0.14    8.13
doubletCells       6.21   0.31    6.66
computeSumFactors  6.00   0.25    6.25
convertTo          4.93   0.19    5.12
** running examples for arch 'x64' ... WARNING
Found the following significant warnings:

  Warning: handling of spike-ins via 'isSpike()' is deprecated.
  Warning: 'normalizeSCE' is deprecated.
  Warning: 'centreSizeFactors' is deprecated.
  Warning: 'trendVar' is deprecated.
  Warning: 'decomposeVar' is deprecated.
  Warning: 'testVar' is deprecated.
  Warning: 'trendVar' is deprecated.
  Warning: 'decomposeVar' is deprecated.
  Warning: 'testVar' is deprecated.
  Warning: 'normalizeSCE' is deprecated.
  Warning: 'centreSizeFactors' is deprecated.
  Warning: 'clusters=' is deprecated.
  Warning: 'improvedCV2' is deprecated.
  Warning: handling of spike-ins via 'isSpike()' is deprecated.
  Warning: 'multiBlockNorm' is deprecated.
  Warning: 'normalizeSCE' is deprecated.
  Warning: handling of spike-ins via 'isSpike()' is deprecated.
  Warning: 'multiBlockNorm' is deprecated.
  Warning: 'normalizeSCE' is deprecated.
  Warning: 'multiBlockVar' is deprecated.
  Warning: 'type=' is deprecated.
  Warning: 'trendVar' is deprecated.
  Warning: 'decomposeVar' is deprecated.
  Warning: 'testVar' is deprecated.
  Warning: 'type=' is deprecated.
  Warning: 'trendVar' is deprecated.
  Warning: 'decomposeVar' is deprecated.
  Warning: 'testVar' is deprecated.
  Warning: 'type=' is deprecated.
  Warning: 'trendVar' is deprecated.
  Warning: 'decomposeVar' is deprecated.
  Warning: 'testVar' is deprecated.
  Warning: 'isSpike' is deprecated.
  Warning: 'normalizeSCE' is deprecated.
  Warning: 'centreSizeFactors' is deprecated.
  Warning: handling of spike-ins via 'isSpike()' is deprecated.
  Warning: 'overlapExprs' is deprecated.
  Warning: 'parallelPCA' is deprecated.
  Warning: 'technicalCV2' is deprecated.
  Warning: 'isSpike<-' is deprecated.
  Warning: 'spikeNames' is deprecated.
  Warning: 'isSpike' is deprecated.
  Warning: 'technicalCV2' is deprecated.
  Warning: 'testVar' is deprecated.
  Warning: 'testVar' is deprecated.
  Warning: 'testVar' is deprecated.
  Warning: handling of spike-ins via 'isSpike()' is deprecated.
  Warning: 'normalizeSCE' is deprecated.
  Warning: 'centreSizeFactors' is deprecated.
  Warning: 'trendVar' is deprecated.
  Warning: 'trendVar' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Examples with CPU or elapsed time > 5s
                   user system elapsed
cyclone           13.72   0.39   14.11
bootstrapCluster  11.34   0.25   11.59
doubletCells       6.12   0.22    6.36
computeSumFactors  5.30   0.22    5.51
trendVar           1.13   0.04   23.39
technicalCV2       0.39   0.00    8.96
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  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: 2 WARNINGs, 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.10-bioc/meat/scran.Rcheck/00check.log'
for details.



Installation output

scran.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/scran_1.14.6.tar.gz && rm -rf scran.buildbin-libdir && mkdir scran.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=scran.buildbin-libdir scran_1.14.6.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL scran_1.14.6.zip && rm scran_1.14.6.tar.gz scran_1.14.6.zip
###
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                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  571k  100  571k    0     0  7075k      0 --:--:-- --:--:-- --:--:-- 7417k

install for i386

* installing *source* package 'scran' ...
** using staged installation
** libs
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/beachmat/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/dqrng/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/beachmat/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/dqrng/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c build_snn.cpp -o build_snn.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/beachmat/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/dqrng/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c calc_log_count_stats.cpp -o calc_log_count_stats.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/beachmat/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/dqrng/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c combine_rho.cpp -o combine_rho.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/beachmat/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/dqrng/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c combine_simes.cpp -o combine_simes.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/beachmat/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/dqrng/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c compute_CV2.cpp -o compute_CV2.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/beachmat/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/dqrng/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c compute_blocked_stats.cpp -o compute_blocked_stats.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/beachmat/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/dqrng/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c compute_rho_null.cpp -o compute_rho_null.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/beachmat/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/dqrng/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c compute_rho_pairs.cpp -o compute_rho_pairs.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/beachmat/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/dqrng/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c cyclone_scores.cpp -o cyclone_scores.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/beachmat/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/dqrng/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c fit_linear_model.cpp -o fit_linear_model.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/beachmat/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/dqrng/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c get_residuals.cpp -o get_residuals.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/beachmat/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/dqrng/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c get_scaled_ranks.cpp -o get_scaled_ranks.o
get_scaled_ranks.cpp: In instantiation of 'SEXPREC* average_ranks_internal(SEXP, SEXP, SEXP, SEXP) [with M = beachmat::lin_matrix<int, Rcpp::Vector<13> >; SEXP = SEXPREC*]':
get_scaled_ranks.cpp:137:100:   required from here
get_scaled_ranks.cpp:67:16: warning: unused variable 'accumulated_rank' [-Wunused-variable]
         double accumulated_rank=0;
                ^
get_scaled_ranks.cpp: In instantiation of 'SEXPREC* average_ranks_internal(SEXP, SEXP, SEXP, SEXP) [with M = beachmat::lin_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >; SEXP = SEXPREC*]':
get_scaled_ranks.cpp:139:100:   required from here
get_scaled_ranks.cpp:67:16: warning: unused variable 'accumulated_rank' [-Wunused-variable]
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/beachmat/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/dqrng/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c overlap_exprs.cpp -o overlap_exprs.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/beachmat/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/dqrng/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c pool_size_factors.cpp -o pool_size_factors.o
pool_size_factors.cpp: In function 'Rcpp::List pool_size_factors(Rcpp::RObject, Rcpp::NumericVector, Rcpp::IntegerVector, Rcpp::IntegerVector)':
pool_size_factors.cpp:36:15: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (ngenes!=pseudo_cell.size()) { throw std::runtime_error("length of pseudo-cell vector is not the same as the number of cells"); }
               ^
pool_size_factors.cpp:39:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (order.size() < ncells*2-1)  { throw std::runtime_error("ordering vector is too short for number of cells"); }
                      ^
pool_size_factors.cpp:101:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                     for (auto i=0; i<n; ++i, ++val, ++idx) {
                                     ^
In file included from pool_size_factors.cpp:4:0:
C:/Users/biocbuild/bbs-3.10-bioc/R/library/beachmat/include/beachmat/utils/const_column.h: In instantiation of 'Rcpp::traits::storage_type<13>::type* beachmat::const_column<M>::get_indices() [with M = beachmat::lin_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >; Rcpp::Vector<13>::iterator = int*; Rcpp::traits::storage_type<13>::type = int]':
pool_size_factors.cpp:52:34:   required from here
C:/Users/biocbuild/bbs-3.10-bioc/R/library/beachmat/include/beachmat/utils/const_column.h:66:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (ref->get_nrow() > indices.size()) {
                             ^
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/beachmat/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/dqrng/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c rand_custom.cpp -o rand_custom.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/beachmat/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/dqrng/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c run_dormqr.cpp -o run_dormqr.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/beachmat/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/dqrng/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c shuffle_matrix.cpp -o shuffle_matrix.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/beachmat/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/dqrng/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c subset_and_divide.cpp -o subset_and_divide.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/beachmat/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/dqrng/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c utils.cpp -o utils.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o scran.dll tmp.def RcppExports.o build_snn.o calc_log_count_stats.o combine_rho.o combine_simes.o compute_CV2.o compute_blocked_stats.o compute_rho_null.o compute_rho_pairs.o cyclone_scores.o fit_linear_model.o get_residuals.o get_scaled_ranks.o overlap_exprs.o pool_size_factors.o rand_custom.o run_dormqr.o shuffle_matrix.o subset_and_divide.o utils.o -LC:/Users/BIOCBU~1/BBS-3~1.10-/R/bin/i386 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.10-/R/bin/i386 -lRblas -lgfortran -lm -lquadmath -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.10-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.10-bioc/meat/scran.buildbin-libdir/00LOCK-scran/00new/scran/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'scran'
    finding HTML links ... done
    DM                                      html  
    bootstrapCluster                        html  
    finding level-2 HTML links ... done

    buildSNNGraph                           html  
    cleanSizeFactors                        html  
    clusterModularity                       html  
    combineMarkers                          html  
    combinePValues                          html  
    combineVar                              html  
    computeSpikeFactors                     html  
    computeSumFactors                       html  
    convertTo                               html  
    correlateGenes                          html  
    correlateNull                           html  
    correlatePairs                          html  
    cyclone                                 html  
    decomposeVar                            html  
    denoisePCA                              html  
    doubletCells                            html  
    doubletCluster                          html  
    findMarkers                             html  
    fitTrendCV2                             html  
    fitTrendPoisson                         html  
    fitTrendVar                             html  
    gene_selection                          html  
    getClusteredPCs                         html  
    getTopHVGs                              html  
    getTopMarkers                           html  
    improvedCV2                             html  
    makeTechTrend                           html  
    modelGeneCV2                            html  
    modelGeneCV2WithSpikes                  html  
    modelGeneVar                            html  
    modelGeneVarByPoisson                   html  
    modelGeneVarWithSpikes                  html  
    multiBlockNorm                          html  
    multiBlockVar                           html  
    overlapExprs                            html  
    pairwiseBinom                           html  
    pairwiseTTests                          html  
    pairwiseWilcox                          html  
    parallelPCA                             html  
    quickCluster                            html  
    quickSubCluster                         html  
    sandbag                                 html  
    scaledColRanks                          html  
    technicalCV2                            html  
    testVar                                 html  
    trendVar                                html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'scran' ...
** libs
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/beachmat/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/dqrng/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/beachmat/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/dqrng/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c build_snn.cpp -o build_snn.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/beachmat/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/dqrng/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c calc_log_count_stats.cpp -o calc_log_count_stats.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/beachmat/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/dqrng/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c combine_rho.cpp -o combine_rho.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/beachmat/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/dqrng/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c combine_simes.cpp -o combine_simes.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/beachmat/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/dqrng/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c compute_CV2.cpp -o compute_CV2.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/beachmat/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/dqrng/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c compute_blocked_stats.cpp -o compute_blocked_stats.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/beachmat/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/dqrng/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c compute_rho_null.cpp -o compute_rho_null.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/beachmat/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/dqrng/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c compute_rho_pairs.cpp -o compute_rho_pairs.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/beachmat/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/dqrng/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c cyclone_scores.cpp -o cyclone_scores.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/beachmat/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/dqrng/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c fit_linear_model.cpp -o fit_linear_model.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/beachmat/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/dqrng/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c get_residuals.cpp -o get_residuals.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/beachmat/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/dqrng/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c get_scaled_ranks.cpp -o get_scaled_ranks.o
get_scaled_ranks.cpp: In instantiation of 'SEXPREC* average_ranks_internal(SEXP, SEXP, SEXP, SEXP) [with M = beachmat::lin_matrix<int, Rcpp::Vector<13> >; SEXP = SEXPREC*]':
get_scaled_ranks.cpp:137:100:   required from here
get_scaled_ranks.cpp:67:16: warning: unused variable 'accumulated_rank' [-Wunused-variable]
         double accumulated_rank=0;
                ^
get_scaled_ranks.cpp: In instantiation of 'SEXPREC* average_ranks_internal(SEXP, SEXP, SEXP, SEXP) [with M = beachmat::lin_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >; SEXP = SEXPREC*]':
get_scaled_ranks.cpp:139:100:   required from here
get_scaled_ranks.cpp:67:16: warning: unused variable 'accumulated_rank' [-Wunused-variable]
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/beachmat/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/dqrng/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c overlap_exprs.cpp -o overlap_exprs.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/beachmat/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/dqrng/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c pool_size_factors.cpp -o pool_size_factors.o
pool_size_factors.cpp: In function 'Rcpp::List pool_size_factors(Rcpp::RObject, Rcpp::NumericVector, Rcpp::IntegerVector, Rcpp::IntegerVector)':
pool_size_factors.cpp:36:15: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (ngenes!=pseudo_cell.size()) { throw std::runtime_error("length of pseudo-cell vector is not the same as the number of cells"); }
               ^
pool_size_factors.cpp:39:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (order.size() < ncells*2-1)  { throw std::runtime_error("ordering vector is too short for number of cells"); }
                      ^
pool_size_factors.cpp:101:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                     for (auto i=0; i<n; ++i, ++val, ++idx) {
                                     ^
In file included from pool_size_factors.cpp:4:0:
C:/Users/biocbuild/bbs-3.10-bioc/R/library/beachmat/include/beachmat/utils/const_column.h: In instantiation of 'Rcpp::traits::storage_type<13>::type* beachmat::const_column<M>::get_indices() [with M = beachmat::lin_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >; Rcpp::Vector<13>::iterator = int*; Rcpp::traits::storage_type<13>::type = int]':
pool_size_factors.cpp:52:34:   required from here
C:/Users/biocbuild/bbs-3.10-bioc/R/library/beachmat/include/beachmat/utils/const_column.h:66:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (ref->get_nrow() > indices.size()) {
                             ^
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/beachmat/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/dqrng/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c rand_custom.cpp -o rand_custom.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/beachmat/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/dqrng/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c run_dormqr.cpp -o run_dormqr.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/beachmat/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/dqrng/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c shuffle_matrix.cpp -o shuffle_matrix.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/beachmat/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/dqrng/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c subset_and_divide.cpp -o subset_and_divide.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/beachmat/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/dqrng/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c utils.cpp -o utils.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o scran.dll tmp.def RcppExports.o build_snn.o calc_log_count_stats.o combine_rho.o combine_simes.o compute_CV2.o compute_blocked_stats.o compute_rho_null.o compute_rho_pairs.o cyclone_scores.o fit_linear_model.o get_residuals.o get_scaled_ranks.o overlap_exprs.o pool_size_factors.o rand_custom.o run_dormqr.o shuffle_matrix.o subset_and_divide.o utils.o -LC:/Users/BIOCBU~1/BBS-3~1.10-/R/bin/x64 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.10-/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.10-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.10-bioc/meat/scran.buildbin-libdir/scran/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'scran' as scran_1.14.6.zip
* DONE (scran)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'scran' successfully unpacked and MD5 sums checked

Tests output

scran.Rcheck/tests_i386/testthat.Rout


R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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: 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, 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, 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

Attaching package: 'IRanges'

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    windows

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'

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    anyMissing, rowMedians

Loading required package: BiocParallel

Attaching package: 'DelayedArray'

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    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

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

    aperm, apply, rowsum

> test_check("scran")
== testthat results  ===========================================================
[ OK: 5757 | SKIPPED: 3 | WARNINGS: 843 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 257.65    7.60  266.25 

scran.Rcheck/tests_x64/testthat.Rout


R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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'

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    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, 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, 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

Attaching package: 'IRanges'

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

    windows

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: 5757 | SKIPPED: 3 | WARNINGS: 843 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 244.68    5.40  251.59 

Example timings

scran.Rcheck/examples_i386/scran-Ex.timings

nameusersystemelapsed
DM0.090.000.10
bootstrapCluster14.46 0.5215.14
buildSNNGraph7.990.148.13
cleanSizeFactors0.060.000.06
clusterModularity2.070.082.15
combineMarkers1.720.001.72
combinePValues0.060.000.06
combineVar1.960.011.97
computeSpikeFactors0.840.020.86
computeSumFactors6.000.256.25
convertTo4.930.195.12
correlateGenes1.150.001.14
correlateNull0.230.000.24
correlatePairs1.850.031.89
cyclone20.23 0.7521.00
decomposeVar1.990.092.09
denoisePCA1.790.001.78
doubletCells6.210.316.66
doubletCluster0.550.000.55
findMarkers2.090.022.11
fitTrendCV21.170.061.33
fitTrendPoisson0.380.000.37
fitTrendVar0.690.030.72
getClusteredPCs3.420.554.00
getTopHVGs0.760.000.76
getTopMarkers0.970.031.00
improvedCV20.380.020.40
makeTechTrend0.060.000.06
modelGeneCV21.110.061.17
modelGeneCV2WithSpikes0.940.000.94
modelGeneVar1.090.091.18
modelGeneVarByPoisson1.090.031.13
modelGeneVarWithSpikes1.010.021.03
multiBlockNorm1.470.081.54
multiBlockVar1.770.081.85
overlapExprs1.080.011.09
pairwiseBinom0.750.000.75
pairwiseTTests0.900.020.92
pairwiseWilcox0.860.030.89
parallelPCA1.570.111.68
quickCluster2.670.002.71
quickSubCluster4.330.064.39
sandbag0.810.000.90
scaledColRanks2.480.002.49
technicalCV20.690.030.72
testVar0.060.000.06
trendVar1.550.051.59

scran.Rcheck/examples_x64/scran-Ex.timings

nameusersystemelapsed
DM0.050.000.05
bootstrapCluster11.34 0.2511.59
buildSNNGraph4.670.084.75
cleanSizeFactors0.030.000.06
clusterModularity1.500.011.52
combineMarkers1.300.001.31
combinePValues0.050.000.05
combineVar1.330.001.33
computeSpikeFactors0.670.000.67
computeSumFactors5.300.225.51
convertTo4.100.084.19
correlateGenes1.000.031.03
correlateNull0.270.000.27
correlatePairs1.940.031.97
cyclone13.72 0.3914.11
decomposeVar1.950.052.04
denoisePCA1.640.031.68
doubletCells6.120.226.36
doubletCluster0.660.000.66
findMarkers2.510.002.51
fitTrendCV20.50.00.5
fitTrendPoisson1.390.061.46
fitTrendVar0.740.000.73
getClusteredPCs4.200.074.27
getTopHVGs0.910.000.90
getTopMarkers1.080.011.10
improvedCV20.330.020.34
makeTechTrend0.060.000.07
modelGeneCV21.690.061.75
modelGeneCV2WithSpikes0.980.000.98
modelGeneVar1.350.021.36
modelGeneVarByPoisson1.190.011.20
modelGeneVarWithSpikes0.880.020.89
multiBlockNorm1.040.041.09
multiBlockVar1.970.072.04
overlapExprs1.140.021.16
pairwiseBinom0.580.000.58
pairwiseTTests0.730.010.75
pairwiseWilcox0.550.000.55
parallelPCA1.180.071.25
quickCluster1.860.031.89
quickSubCluster3.050.033.08
sandbag0.530.000.53
scaledColRanks1.220.001.22
technicalCV20.390.008.96
testVar0.040.000.04
trendVar 1.13 0.0423.39