Back to Multiple platform build/check report for BioC 3.7
ABCDEFGHIJKLMNOPQR[S]TUVWXYZ

CHECK report for scater on tokay2

This page was generated on 2018-10-17 08:41:42 -0400 (Wed, 17 Oct 2018).

Package 1320/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
scater 1.8.4
Davis McCarthy
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/scater
Branch: RELEASE_3_7
Last Commit: d560a9a
Last Changed Date: 2018-08-13 06:13:02 -0400 (Mon, 13 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: scater
Version: 1.8.4
Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:scater.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings scater_1.8.4.tar.gz
StartedAt: 2018-10-17 04:40:46 -0400 (Wed, 17 Oct 2018)
EndedAt: 2018-10-17 04:49:28 -0400 (Wed, 17 Oct 2018)
EllapsedTime: 521.4 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: scater.Rcheck
Warnings: 3

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:scater.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings scater_1.8.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/scater.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'scater/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'scater' 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 whether package 'scater' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpesBNfT/R.INSTALLd84528f6e9c/scater/man/plotReducedDim.Rd:21: file link 'plotPCA' in package 'scater' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpesBNfT/R.INSTALLd84528f6e9c/scater/man/runDiffusionMap.Rd:25: file link 'DiffusionMap' in package 'destiny' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpesBNfT/R.INSTALLd84528f6e9c/scater/man/runDiffusionMap.Rd:33: file link 'DiffusionMap' in package 'destiny' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpesBNfT/R.INSTALLd84528f6e9c/scater/man/runDiffusionMap.Rd:43: file link 'DiffusionMap' in package 'destiny' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpesBNfT/R.INSTALLd84528f6e9c/scater/man/runDiffusionMap.Rd:67: file link 'plotDiffusionMap' in package 'scater' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpesBNfT/R.INSTALLd84528f6e9c/scater/man/runMDS.Rd:62: file link 'plotMDS' in package 'scater' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpesBNfT/R.INSTALLd84528f6e9c/scater/man/runPCA.Rd:84: file link 'plotPCA' in package 'scater' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpesBNfT/R.INSTALLd84528f6e9c/scater/man/runTSNE.Rd:81: file link 'plotTSNE' in package 'scater' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.7-bioc/meat/scater.Rcheck/00install.out' for details.
* checking installed package size ... NOTE
  installed size is 13.6Mb
  sub-directories of 1Mb or more:
    extdata   2.9Mb
    libs      8.6Mb
* 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... 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-3.7-bioc/R/library/scater/libs/i386/scater.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: 'read10xResults' is deprecated.
  Warning: 'downsampleCounts' is deprecated.
  Warning: 'normalizeExprs' is deprecated.
  Warning: 'normalizeExprs' is deprecated.
  Warning: 'normalizeExprs' is deprecated.
  Warning: 'normalizeExprs' is deprecated.
  Warning: 'normalizeExprs' is deprecated.
  Warning: 'normalizeExprs' is deprecated.
  Warning: 'read10xResults' 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
plot_reddim 6.49    0.1     7.5
** running examples for arch 'x64' ... WARNING
Found the following significant warnings:

  Warning: 'read10xResults' is deprecated.
  Warning: 'downsampleCounts' is deprecated.
  Warning: 'normalizeExprs' is deprecated.
  Warning: 'normalizeExprs' is deprecated.
  Warning: 'normalizeExprs' is deprecated.
  Warning: 'normalizeExprs' is deprecated.
  Warning: 'normalizeExprs' is deprecated.
  Warning: 'normalizeExprs' is deprecated.
  Warning: 'read10xResults' 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
plot_reddim 5.25   0.11    5.54
* 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: 3 WARNINGs, 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.7-bioc/meat/scater.Rcheck/00check.log'
for details.

Installation output

scater.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/scater_1.8.4.tar.gz && rm -rf scater.buildbin-libdir && mkdir scater.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=scater.buildbin-libdir scater_1.8.4.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL scater_1.8.4.zip && rm scater_1.8.4.tar.gz scater_1.8.4.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 2862k  100 2862k    0     0  31.7M      0 --:--:-- --:--:-- --:--:-- 34.0M

install for i386

* installing *source* package 'scater' ...
** libs
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c calc_exprs.cpp -o calc_exprs.o
calc_exprs.cpp: In instantiation of 'Rcpp::RObject calc_exprs_internal(M, Rcpp::List, Rcpp::IntegerVector, Rcpp::RObject, Rcpp::RObject, Rcpp::RObject, Rcpp::RObject) [with T = int; V = Rcpp::Vector<13>; M = beachmat::lin_matrix<int, Rcpp::Vector<13> >*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>; Rcpp::List = Rcpp::Vector<19>; Rcpp::IntegerVector = Rcpp::Vector<13>]':
calc_exprs.cpp:132:120:   required from here
calc_exprs.cpp:23:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (sfIt->size() != ncells) { 
                          ^
calc_exprs.cpp:30:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (sf_to_use.size()!=ngenes) { 
                         ^
calc_exprs.cpp:37:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (current < 1 || current > nsfsets) { 
                                    ^
calc_exprs.cpp: In instantiation of 'Rcpp::RObject calc_exprs_internal(M, Rcpp::List, Rcpp::IntegerVector, Rcpp::RObject, Rcpp::RObject, Rcpp::RObject, Rcpp::RObject) [with T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; M = beachmat::lin_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>; Rcpp::List = Rcpp::Vector<19>; Rcpp::IntegerVector = Rcpp::Vector<13>]':
calc_exprs.cpp:135:123:   required from here
calc_exprs.cpp:23:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (sfIt->size() != ncells) { 
                          ^
calc_exprs.cpp:30:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (sf_to_use.size()!=ngenes) { 
                         ^
calc_exprs.cpp:37:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (current < 1 || current > nsfsets) { 
                                    ^
In file included from C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include/beachmat/LIN_matrix.h:174:0,
                 from C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include/beachmat/integer_matrix.h:4,
                 from scater.h:5,
                 from calc_exprs.cpp:1:
C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include/beachmat/LIN_methods.h: In instantiation of 'beachmat::const_col_indexed_info<V> beachmat::lin_matrix<T, V>::get_const_col_indexed(size_t, typename V::iterator, size_t, size_t) [with T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; beachmat::const_col_indexed_info<V> = std::tuple<unsigned int, int*, double*>; typename V::iterator = double*; size_t = unsigned int; typename V::iterator = double*]':
calc_exprs.cpp:140:1:   required from here
C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include/beachmat/LIN_methods.h:58:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (indices.size()!=this->get_nrow()) {
                       ^
C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include/beachmat/LIN_methods.h: In instantiation of 'beachmat::const_col_indexed_info<V> beachmat::lin_matrix<T, V>::get_const_col_indexed(size_t, typename V::iterator, size_t, size_t) [with T = int; V = Rcpp::Vector<13>; beachmat::const_col_indexed_info<V> = std::tuple<unsigned int, int*, int*>; typename V::iterator = int*; size_t = unsigned int; typename V::iterator = int*]':
calc_exprs.cpp:140:1:   required from here
C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include/beachmat/LIN_methods.h:58:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c calc_top_features.cpp -o calc_top_features.o
calc_top_features.cpp: In instantiation of 'Rcpp::RObject calc_top_features_internal(M, Rcpp::RObject, Rcpp::RObject) [with T = int; V = Rcpp::Vector<13>; M = beachmat::lin_matrix<int, Rcpp::Vector<13> >*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]':
calc_top_features.cpp:83:91:   required from here
calc_top_features.cpp:27:44: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (ntop && (top[0] < 1 || top[ntop-1] > used_genes)) {
                                            ^
calc_top_features.cpp:61:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             while (x<=target_index && x<survivors.size()) {
                                        ^
calc_top_features.cpp: In instantiation of 'Rcpp::RObject calc_top_features_internal(M, Rcpp::RObject, Rcpp::RObject) [with T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; M = beachmat::lin_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]':
calc_top_features.cpp:86:94:   required from here
calc_top_features.cpp:27:44: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (ntop && (top[0] < 1 || top[ntop-1] > used_genes)) {
                                            ^
calc_top_features.cpp:61:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             while (x<=target_index && x<survivors.size()) {
                                        ^
In file included from C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include/beachmat/LIN_matrix.h:174:0,
                 from C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include/beachmat/integer_matrix.h:4,
                 from scater.h:5,
                 from calc_top_features.cpp:1:
C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include/beachmat/LIN_methods.h: In instantiation of 'beachmat::const_col_indexed_info<V> beachmat::lin_matrix<T, V>::get_const_col_indexed(size_t, typename V::iterator, size_t, size_t) [with T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; beachmat::const_col_indexed_info<V> = std::tuple<unsigned int, int*, double*>; typename V::iterator = double*; size_t = unsigned int; typename V::iterator = double*]':
calc_top_features.cpp:91:1:   required from here
C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include/beachmat/LIN_methods.h:58:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (indices.size()!=this->get_nrow()) {
                       ^
C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include/beachmat/LIN_methods.h: In instantiation of 'beachmat::const_col_indexed_info<V> beachmat::lin_matrix<T, V>::get_const_col_indexed(size_t, typename V::iterator, size_t, size_t) [with T = int; V = Rcpp::Vector<13>; beachmat::const_col_indexed_info<V> = std::tuple<unsigned int, int*, int*>; typename V::iterator = int*; size_t = unsigned int; typename V::iterator = int*]':
calc_top_features.cpp:91:1:   required from here
C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include/beachmat/LIN_methods.h:58:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c init.cpp -o init.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c matrix_stats.cpp -o matrix_stats.o
In file included from C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include/beachmat/LIN_matrix.h:174:0,
                 from C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include/beachmat/integer_matrix.h:4,
                 from scater.h:5,
                 from matrix_stats.cpp:1:
C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include/beachmat/LIN_methods.h: In instantiation of 'beachmat::const_col_indexed_info<V> beachmat::lin_matrix<T, V>::get_const_col_indexed(size_t, typename V::iterator, size_t, size_t) [with T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; beachmat::const_col_indexed_info<V> = std::tuple<unsigned int, int*, double*>; typename V::iterator = double*; size_t = unsigned int; typename V::iterator = double*]':
matrix_stats.cpp:340:1:   required from here
C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include/beachmat/LIN_methods.h:58:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (indices.size()!=this->get_nrow()) {
                       ^
C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include/beachmat/LIN_methods.h: In instantiation of 'beachmat::const_col_indexed_info<V> beachmat::lin_matrix<T, V>::get_const_col_indexed(size_t, typename V::iterator, size_t, size_t) [with T = int; V = Rcpp::Vector<13>; beachmat::const_col_indexed_info<V> = std::tuple<unsigned int, int*, int*>; typename V::iterator = int*; size_t = unsigned int; typename V::iterator = int*]':
matrix_stats.cpp:340:1:   required from here
C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include/beachmat/LIN_methods.h:58:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o scater.dll tmp.def calc_exprs.o calc_top_features.o init.o matrix_stats.o -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/library/beachmat/lib/i386 -lbeachmat -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/library/Rhdf5lib/lib/i386 -lhdf5_cpp -lhdf5 -lszip -lz -lpsapi -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.7-bioc/meat/scater.buildbin-libdir/scater/libs/i386
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for 'mutate' in package 'scater'
Creating a new generic function for 'filter' in package 'scater'
** help
*** installing help indices
  converting help for package 'scater'
    finding HTML links ... done
    SCESet                                  html  
    accessors                               html  
    finding level-2 HTML links ... done

    areSizeFactorsCentred                   html  
    arrange                                 html  
    bootstraps                              html  
    calcAverage                             html  
    calcIsExprs                             html  
    calculateCPM                            html  
    calculateFPKM                           html  
    calculateQCMetrics                      html  
    calculateTPM                            html  
    centreSizeFactors                       html  
    downsampleCounts                        html  
    filter                                  html  
    findImportantPCs                        html  
    getBMFeatureAnnos                       html  
    isOutlier                               html  
    kallisto-wrapper                        html  
    librarySizeFactors                      html  
    multiplot                               html  
    mutate                                  html  
    nexprs                                  html  
    normalize                               html  
    normalizeExprs                          html  
    plotColData                             html  
    plotExplanatoryVariables                html  
    plotExpression                          html  
    plotExprsFreqVsMean                     html  
    plotExprsVsTxLength                     html  
    plotHeatmap                             html  
    plotHighestExprs                        html  
    plotPlatePosition                       html  
    plotQC                                  html  
    plotRLE                                 html  
    plotReducedDim                          html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpesBNfT/R.INSTALLd84528f6e9c/scater/man/plotReducedDim.Rd:21: file link 'plotPCA' in package 'scater' does not exist and so has been treated as a topic
    plotRowData                             html  
    plotScater                              html  
    plot_reddim                             html  
    read10xResults                          html  
    readTxResults                           html  
    rename                                  html  
    runDiffusionMap                         html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpesBNfT/R.INSTALLd84528f6e9c/scater/man/runDiffusionMap.Rd:25: file link 'DiffusionMap' in package 'destiny' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpesBNfT/R.INSTALLd84528f6e9c/scater/man/runDiffusionMap.Rd:33: file link 'DiffusionMap' in package 'destiny' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpesBNfT/R.INSTALLd84528f6e9c/scater/man/runDiffusionMap.Rd:43: file link 'DiffusionMap' in package 'destiny' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpesBNfT/R.INSTALLd84528f6e9c/scater/man/runDiffusionMap.Rd:67: file link 'plotDiffusionMap' in package 'scater' does not exist and so has been treated as a topic
    runMDS                                  html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpesBNfT/R.INSTALLd84528f6e9c/scater/man/runMDS.Rd:62: file link 'plotMDS' in package 'scater' does not exist and so has been treated as a topic
    runPCA                                  html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpesBNfT/R.INSTALLd84528f6e9c/scater/man/runPCA.Rd:84: file link 'plotPCA' in package 'scater' does not exist and so has been treated as a topic
    runTSNE                                 html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpesBNfT/R.INSTALLd84528f6e9c/scater/man/runTSNE.Rd:81: file link 'plotTSNE' in package 'scater' does not exist and so has been treated as a topic
    salmon-wrapper                          html  
    sc_example_cell_info                    html  
    sc_example_counts                       html  
    scater-package                          html  
    scater-plot-args                        html  
    scater-vis-var                          html  
    scater_gui                              html  
    summariseExprsAcrossFeatures            html  
    toSingleCellExperiment                  html  
    uniquifyFeatureNames                    html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'scater' ...
** libs
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c calc_exprs.cpp -o calc_exprs.o
calc_exprs.cpp: In instantiation of 'Rcpp::RObject calc_exprs_internal(M, Rcpp::List, Rcpp::IntegerVector, Rcpp::RObject, Rcpp::RObject, Rcpp::RObject, Rcpp::RObject) [with T = int; V = Rcpp::Vector<13>; M = beachmat::lin_matrix<int, Rcpp::Vector<13> >*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>; Rcpp::List = Rcpp::Vector<19>; Rcpp::IntegerVector = Rcpp::Vector<13>]':
calc_exprs.cpp:132:120:   required from here
calc_exprs.cpp:23:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (sfIt->size() != ncells) { 
                          ^
calc_exprs.cpp:30:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (sf_to_use.size()!=ngenes) { 
                         ^
calc_exprs.cpp:37:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (current < 1 || current > nsfsets) { 
                                    ^
calc_exprs.cpp: In instantiation of 'Rcpp::RObject calc_exprs_internal(M, Rcpp::List, Rcpp::IntegerVector, Rcpp::RObject, Rcpp::RObject, Rcpp::RObject, Rcpp::RObject) [with T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; M = beachmat::lin_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>; Rcpp::List = Rcpp::Vector<19>; Rcpp::IntegerVector = Rcpp::Vector<13>]':
calc_exprs.cpp:135:123:   required from here
calc_exprs.cpp:23:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (sfIt->size() != ncells) { 
                          ^
calc_exprs.cpp:30:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (sf_to_use.size()!=ngenes) { 
                         ^
calc_exprs.cpp:37:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (current < 1 || current > nsfsets) { 
                                    ^
In file included from C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include/beachmat/LIN_matrix.h:174:0,
                 from C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include/beachmat/integer_matrix.h:4,
                 from scater.h:5,
                 from calc_exprs.cpp:1:
C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include/beachmat/LIN_methods.h: In instantiation of 'beachmat::const_col_indexed_info<V> beachmat::lin_matrix<T, V>::get_const_col_indexed(size_t, typename V::iterator, size_t, size_t) [with T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; beachmat::const_col_indexed_info<V> = std::tuple<long long unsigned int, int*, double*>; typename V::iterator = double*; size_t = long long unsigned int; typename V::iterator = double*]':
calc_exprs.cpp:140:1:   required from here
C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include/beachmat/LIN_methods.h:58:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (indices.size()!=this->get_nrow()) {
                       ^
C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include/beachmat/LIN_methods.h: In instantiation of 'beachmat::const_col_indexed_info<V> beachmat::lin_matrix<T, V>::get_const_col_indexed(size_t, typename V::iterator, size_t, size_t) [with T = int; V = Rcpp::Vector<13>; beachmat::const_col_indexed_info<V> = std::tuple<long long unsigned int, int*, int*>; typename V::iterator = int*; size_t = long long unsigned int; typename V::iterator = int*]':
calc_exprs.cpp:140:1:   required from here
C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include/beachmat/LIN_methods.h:58:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c calc_top_features.cpp -o calc_top_features.o
calc_top_features.cpp: In instantiation of 'Rcpp::RObject calc_top_features_internal(M, Rcpp::RObject, Rcpp::RObject) [with T = int; V = Rcpp::Vector<13>; M = beachmat::lin_matrix<int, Rcpp::Vector<13> >*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]':
calc_top_features.cpp:83:91:   required from here
calc_top_features.cpp:27:44: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (ntop && (top[0] < 1 || top[ntop-1] > used_genes)) {
                                            ^
calc_top_features.cpp:61:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             while (x<=target_index && x<survivors.size()) {
                                        ^
calc_top_features.cpp: In instantiation of 'Rcpp::RObject calc_top_features_internal(M, Rcpp::RObject, Rcpp::RObject) [with T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; M = beachmat::lin_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]':
calc_top_features.cpp:86:94:   required from here
calc_top_features.cpp:27:44: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (ntop && (top[0] < 1 || top[ntop-1] > used_genes)) {
                                            ^
calc_top_features.cpp:61:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             while (x<=target_index && x<survivors.size()) {
                                        ^
In file included from C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include/beachmat/LIN_matrix.h:174:0,
                 from C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include/beachmat/integer_matrix.h:4,
                 from scater.h:5,
                 from calc_top_features.cpp:1:
C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include/beachmat/LIN_methods.h: In instantiation of 'beachmat::const_col_indexed_info<V> beachmat::lin_matrix<T, V>::get_const_col_indexed(size_t, typename V::iterator, size_t, size_t) [with T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; beachmat::const_col_indexed_info<V> = std::tuple<long long unsigned int, int*, double*>; typename V::iterator = double*; size_t = long long unsigned int; typename V::iterator = double*]':
calc_top_features.cpp:91:1:   required from here
C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include/beachmat/LIN_methods.h:58:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (indices.size()!=this->get_nrow()) {
                       ^
C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include/beachmat/LIN_methods.h: In instantiation of 'beachmat::const_col_indexed_info<V> beachmat::lin_matrix<T, V>::get_const_col_indexed(size_t, typename V::iterator, size_t, size_t) [with T = int; V = Rcpp::Vector<13>; beachmat::const_col_indexed_info<V> = std::tuple<long long unsigned int, int*, int*>; typename V::iterator = int*; size_t = long long unsigned int; typename V::iterator = int*]':
calc_top_features.cpp:91:1:   required from here
C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include/beachmat/LIN_methods.h:58:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c init.cpp -o init.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c matrix_stats.cpp -o matrix_stats.o
In file included from C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include/beachmat/LIN_matrix.h:174:0,
                 from C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include/beachmat/integer_matrix.h:4,
                 from scater.h:5,
                 from matrix_stats.cpp:1:
C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include/beachmat/LIN_methods.h: In instantiation of 'beachmat::const_col_indexed_info<V> beachmat::lin_matrix<T, V>::get_const_col_indexed(size_t, typename V::iterator, size_t, size_t) [with T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; beachmat::const_col_indexed_info<V> = std::tuple<long long unsigned int, int*, double*>; typename V::iterator = double*; size_t = long long unsigned int; typename V::iterator = double*]':
matrix_stats.cpp:340:1:   required from here
C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include/beachmat/LIN_methods.h:58:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (indices.size()!=this->get_nrow()) {
                       ^
C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include/beachmat/LIN_methods.h: In instantiation of 'beachmat::const_col_indexed_info<V> beachmat::lin_matrix<T, V>::get_const_col_indexed(size_t, typename V::iterator, size_t, size_t) [with T = int; V = Rcpp::Vector<13>; beachmat::const_col_indexed_info<V> = std::tuple<long long unsigned int, int*, int*>; typename V::iterator = int*; size_t = long long unsigned int; typename V::iterator = int*]':
matrix_stats.cpp:340:1:   required from here
C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include/beachmat/LIN_methods.h:58:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o scater.dll tmp.def calc_exprs.o calc_top_features.o init.o matrix_stats.o -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/library/beachmat/lib/x64 -lbeachmat -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/library/Rhdf5lib/lib/x64 -lhdf5_cpp -lhdf5 -lszip -lz -lpsapi -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.7-bioc/meat/scater.buildbin-libdir/scater/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'scater' as scater_1.8.4.zip
* DONE (scater)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'scater' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output

scater.Rcheck/tests_i386/testthat.Rout


R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
Copyright (C) 2018 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.

> Sys.setenv("R_TESTS" = "")
> library(testthat)
> library(scater)
Loading required package: Biobase
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

Welcome to Bioconductor

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

Loading required package: ggplot2
Loading required package: SingleCellExperiment
Loading required package: SummarizedExperiment
Loading required package: GenomicRanges
Loading required package: stats4
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: 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


Attaching package: 'scater'

The following object is masked from 'package:S4Vectors':

    rename

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

    filter

> 
> test_check("scater")
Collapsing expression to 500 features.Collapsing expression to 500 features.Collapsing expression to 500 features.Collapsing expression to 500 features.Collapsing expression to 500 features.Kallisto log not provided - assuming all runs successfulCollapsing expression to 500 features.Kallisto log not provided - assuming all runs successful== testthat results  ===========================================================
OK: 1014 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  67.12    2.32   69.68

scater.Rcheck/tests_x64/testthat.Rout


R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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.

> Sys.setenv("R_TESTS" = "")
> library(testthat)
> library(scater)
Loading required package: Biobase
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

Welcome to Bioconductor

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

Loading required package: ggplot2
Loading required package: SingleCellExperiment
Loading required package: SummarizedExperiment
Loading required package: GenomicRanges
Loading required package: stats4
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: 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


Attaching package: 'scater'

The following object is masked from 'package:S4Vectors':

    rename

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

    filter

> 
> test_check("scater")
Collapsing expression to 500 features.Collapsing expression to 500 features.Collapsing expression to 500 features.Collapsing expression to 500 features.Collapsing expression to 500 features.Kallisto log not provided - assuming all runs successfulCollapsing expression to 500 features.Kallisto log not provided - assuming all runs successful== testthat results  ===========================================================
OK: 1014 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  74.15    1.17   75.31

Example timings

scater.Rcheck/examples_i386/scater-Ex.timings

nameusersystemelapsed
accessors0.580.200.78
areSizeFactorsCentred0.090.020.11
arrange0.090.010.11
bootstraps0.060.010.08
calcAverage0.070.020.07
calcIsExprs0.060.010.08
calculateCPM0.080.020.10
calculateFPKM0.110.010.12
calculateQCMetrics0.970.041.00
calculateTPM0.230.040.28
centreSizeFactors0.100.000.11
downsampleCounts0.380.020.72
filter0.100.000.11
findImportantPCs2.740.092.83
getBMFeatureAnnos000
isOutlier0.700.030.73
kallisto-wrapper000
librarySizeFactors0.000.020.02
multiplot2.200.012.22
mutate0.060.020.08
nexprs0.100.020.11
normalize0.420.010.45
normalizeExprs0.410.050.46
plotColData2.320.062.39
plotExplanatoryVariables1.280.001.28
plotExpression4.600.064.65
plotExprsFreqVsMean1.750.021.77
plotExprsVsTxLength3.950.084.05
plotHeatmap0.910.040.95
plotHighestExprs1.750.071.81
plotPlatePosition1.580.011.60
plotQC2.780.052.82
plotRLE4.150.194.35
plotReducedDim3.360.013.37
plotRowData1.730.031.76
plotScater3.470.033.50
plot_reddim6.490.107.50
read10xResults101
readTxResults000
rename0.070.030.11
runDiffusionMap0.240.030.27
runMDS0.080.020.09
runPCA0.090.010.11
runTSNE0.270.000.27
salmon-wrapper000
scater_gui0.750.020.76
summariseExprsAcrossFeatures0.950.010.97
toSingleCellExperiment000
uniquifyFeatureNames000

scater.Rcheck/examples_x64/scater-Ex.timings

nameusersystemelapsed
accessors1.110.091.20
areSizeFactorsCentred0.130.020.15
arrange0.140.010.15
bootstraps0.080.040.11
calcAverage0.040.030.08
calcIsExprs0.080.010.09
calculateCPM0.080.020.10
calculateFPKM0.140.010.15
calculateQCMetrics0.880.050.93
calculateTPM0.210.030.25
centreSizeFactors0.100.030.12
downsampleCounts0.300.000.29
filter0.080.020.10
findImportantPCs2.180.052.22
getBMFeatureAnnos000
isOutlier0.440.010.45
kallisto-wrapper0.010.000.02
librarySizeFactors000
multiplot2.250.032.28
mutate0.060.030.10
nexprs0.110.000.11
normalize0.390.040.42
normalizeExprs0.460.040.50
plotColData2.550.002.57
plotExplanatoryVariables2.080.032.11
plotExpression3.50.03.5
plotExprsFreqVsMean1.360.021.38
plotExprsVsTxLength3.640.013.65
plotHeatmap1.310.021.33
plotHighestExprs1.490.031.52
plotPlatePosition1.250.001.25
plotQC2.800.032.83
plotRLE3.970.054.02
plotReducedDim3.970.013.99
plotRowData1.640.001.64
plotScater3.080.033.11
plot_reddim5.250.115.54
read10xResults0.140.000.14
readTxResults000
rename0.090.010.11
runDiffusionMap0.190.020.20
runMDS0.120.010.14
runPCA0.110.000.11
runTSNE0.250.020.27
salmon-wrapper000
scater_gui0.640.020.65
summariseExprsAcrossFeatures0.900.010.91
toSingleCellExperiment000
uniquifyFeatureNames000