Multiple platform build/check report for BioC 3.6 - CHECK report for scater on tokay1

Package: scater

Version: 1.6.3

Command: rm -rf scater.buildbin-libdir scater.Rcheck && mkdir scater.buildbin-libdir scater.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=scater.buildbin-libdir scater_1.6.3.tar.gz >scater.Rcheck\00install.out 2>&1 && cp scater.Rcheck\00install.out scater-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=scater.buildbin-libdir --install="check:scater-install.out" --force-multiarch --no-vignettes --timings scater_1.6.3.tar.gz

StartedAt: 2018-04-12 03:00:07 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 03:10:01 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 594.5 seconds

RetCode: 0

Status: WARNINGS

CheckDir: scater.Rcheck

Warnings: 1

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf scater.buildbin-libdir scater.Rcheck && mkdir scater.buildbin-libdir scater.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=scater.buildbin-libdir scater_1.6.3.tar.gz >scater.Rcheck\00install.out 2>&1 && cp scater.Rcheck\00install.out scater-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=scater.buildbin-libdir --install="check:scater-install.out" --force-multiarch --no-vignettes --timings scater_1.6.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/scater.Rcheck'
* using R version 3.4.4 (2018-03-15)
* 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 '1.6.3'
* 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-3.6-bioc/tmpdir/Rtmp2tCbIT/R.INSTALL3af867d373ef/scater/man/plotDiffusionMap.Rd:64: missing file link 'DiffusionMap'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2tCbIT/R.INSTALL3af867d373ef/scater/man/plotDiffusionMap.Rd:66: missing file link 'DiffusionMap'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2tCbIT/R.INSTALL3af867d373ef/scater/man/plotDiffusionMap.Rd:68: missing file link 'DiffusionMap'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2tCbIT/R.INSTALL3af867d373ef/scater/man/plotDiffusionMap.Rd:107: missing file link 'DiffusionMap'
See 'C:/Users/biocbuild/bbs-3.6-bioc/meat/scater.Rcheck/00install.out' for details.
* checking installed package size ... NOTE
  installed size is 17.1Mb
  sub-directories of 1Mb or more:
    doc       3.8Mb
    extdata   2.9Mb
    libs      8.5Mb
* 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-3.6-bioc/meat/scater.buildbin-libdir/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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                user system elapsed
plotExpression 10.19   0.05   10.25
plotRLE         7.14   0.30    7.44
plotPCA         6.37   0.05    6.42
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                user system elapsed
plotExpression 11.28   0.04   11.33
plotPCA         6.17   0.00    6.18
plotRLE         5.61   0.25    5.86
* 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: 1 WARNING, 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/scater.Rcheck/00check.log'
for details.


install for i386

* installing *source* package 'scater' ...
** libs
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rhdf5lib/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/beachmat/include"   -I"C:/local323/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:125:120:   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: 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:128:123:   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) { 
                         ^
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rhdf5lib/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/beachmat/include"   -I"C:/local323/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()) {
                                        ^
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rhdf5lib/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/beachmat/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c calc_variance.cpp -o calc_variance.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rhdf5lib/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/beachmat/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c downsample_matrix.cpp -o downsample_matrix.o
downsample_matrix.cpp: In instantiation of 'void downsample_matrix_internal(M, O, Rcpp::NumericVector) [with M = beachmat::lin_matrix<int, Rcpp::Vector<13> >*; O = beachmat::lin_output<int>*; Rcpp::NumericVector = Rcpp::Vector<14, Rcpp::PreserveStorage>]':
downsample_matrix.cpp:72:62:   required from here
downsample_matrix.cpp:9:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (prop.size()!=ncells) {
                    ^
downsample_matrix.cpp: In instantiation of 'void downsample_matrix_internal(M, O, Rcpp::NumericVector) [with M = beachmat::lin_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >*; O = beachmat::lin_output<double>*; Rcpp::NumericVector = Rcpp::Vector<14, Rcpp::PreserveStorage>]':
downsample_matrix.cpp:77:62:   required from here
downsample_matrix.cpp:9:20: 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˜1.6-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rhdf5lib/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/beachmat/include"   -I"C:/local323/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˜1.6-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rhdf5lib/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/beachmat/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c margin_summary.cpp -o margin_summary.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o scater.dll tmp.def calc_exprs.o calc_top_features.o calc_variance.o downsample_matrix.o init.o margin_summary.o -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/library/beachmat/lib/i386 -lbeachmat -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/library/Rhdf5lib/lib/i386 -lhdf5_cpp -lhdf5 -lszip -lz -lpsapi -LC:/local323/lib/i386 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/scater.buildbin-libdir/scater/libs/i386
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing 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  
    deprecated                              html  
    downsampleCounts                        html  
    filter                                  html  
    findImportantPCs                        html  
    getBMFeatureAnnos                       html  
    isOutlier                               html  
    kallisto-wrapper                        html  
    multiplot                               html  
    mutate                                  html  
    newSCESet                               html  
    nexprs                                  html  
    normaliseExprs                          html  
    normalize                               html  
    plotDiffusionMap                        html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2tCbIT/R.INSTALL3af867d373ef/scater/man/plotDiffusionMap.Rd:64: missing file link 'DiffusionMap'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2tCbIT/R.INSTALL3af867d373ef/scater/man/plotDiffusionMap.Rd:66: missing file link 'DiffusionMap'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2tCbIT/R.INSTALL3af867d373ef/scater/man/plotDiffusionMap.Rd:68: missing file link 'DiffusionMap'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2tCbIT/R.INSTALL3af867d373ef/scater/man/plotDiffusionMap.Rd:107: missing file link 'DiffusionMap'
    plotExplanatoryVariables                html  
    plotExpression                          html  
    plotExprsFreqVsMean                     html  
    plotExprsVsTxLength                     html  
    plotFeatureData                         html  
    plotHighestExprs                        html  
    plotMDS                                 html  
    plotMetadata                            html  
    plotPCA                                 html  
    plotPhenoData                           html  
    plotPlatePosition                       html  
    plotQC                                  html  
    plotRLE                                 html  
    plotReducedDim                          html  
    plotScater                              html  
    plotTSNE                                html  
    read10XResults                          html  
    readTxResults                           html  
    rename                                  html  
    salmon-wrapper                          html  
    sc_example_cell_info                    html  
    sc_example_counts                       html  
    scater-package                          html  
    scater_gui                              html  
    summariseExprsAcrossFeatures            html  
    toSingleCellExperiment                  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˜1.6-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rhdf5lib/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/beachmat/include"   -I"C:/local323/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:125:120:   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: 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:128:123:   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) { 
                         ^
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rhdf5lib/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/beachmat/include"   -I"C:/local323/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()) {
                                        ^
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rhdf5lib/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/beachmat/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c calc_variance.cpp -o calc_variance.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rhdf5lib/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/beachmat/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c downsample_matrix.cpp -o downsample_matrix.o
downsample_matrix.cpp: In instantiation of 'void downsample_matrix_internal(M, O, Rcpp::NumericVector) [with M = beachmat::lin_matrix<int, Rcpp::Vector<13> >*; O = beachmat::lin_output<int>*; Rcpp::NumericVector = Rcpp::Vector<14, Rcpp::PreserveStorage>]':
downsample_matrix.cpp:72:62:   required from here
downsample_matrix.cpp:9:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (prop.size()!=ncells) {
                    ^
downsample_matrix.cpp: In instantiation of 'void downsample_matrix_internal(M, O, Rcpp::NumericVector) [with M = beachmat::lin_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >*; O = beachmat::lin_output<double>*; Rcpp::NumericVector = Rcpp::Vector<14, Rcpp::PreserveStorage>]':
downsample_matrix.cpp:77:62:   required from here
downsample_matrix.cpp:9:20: 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˜1.6-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rhdf5lib/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/beachmat/include"   -I"C:/local323/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˜1.6-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rhdf5lib/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/beachmat/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c margin_summary.cpp -o margin_summary.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o scater.dll tmp.def calc_exprs.o calc_top_features.o calc_variance.o downsample_matrix.o init.o margin_summary.o -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/library/beachmat/lib/x64 -lbeachmat -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/library/Rhdf5lib/lib/x64 -lhdf5_cpp -lhdf5 -lszip -lz -lpsapi -LC:/local323/lib/x64 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/scater.buildbin-libdir/scater/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'scater' as scater_1.6.3.zip
* DONE (scater)
In R CMD INSTALL
In R CMD INSTALL


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
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, cbind, colMeans, colSums, colnames, 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
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


Attaching package: 'DelayedArray'

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

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

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

    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: 278 SKIPPED: 1 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  33.92    1.48   35.40


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
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, cbind, colMeans, colSums, colnames, 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
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


Attaching package: 'DelayedArray'

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

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

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

    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: 278 SKIPPED: 1 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  30.96    1.29   32.25

name	user	system	elapsed
accessors	1.29	0.05	1.34
areSizeFactorsCentred	0.26	0.00	0.26
arrange	0.10	0.01	0.11
bootstraps	0.09	0.00	0.10
calcAverage	0.05	0.00	0.04
calcIsExprs	0.05	0.00	0.05
calculateCPM	0.06	0.00	0.06
calculateFPKM	0.07	0.00	0.06
calculateQCMetrics	0.61	0.03	0.66
calculateTPM	0.60	0.03	0.64
deprecated	0	0	0
downsampleCounts	0.33	0.02	0.34
filter	0.17	0.00	0.17
findImportantPCs	3.66	0.11	3.77
getBMFeatureAnnos	0	0	0
isOutlier	0.15	0.03	0.19
kallisto-wrapper	0	0	0
multiplot	3.99	0.03	4.02
mutate	0.06	0.02	0.07
newSCESet	0.03	0.01	0.05
nexprs	0.04	0.02	0.06
normaliseExprs	0.44	0.05	0.48
normalize	1.07	0.01	1.09
plotDiffusionMap	0.27	0.00	0.27
plotExplanatoryVariables	1.61	0.05	1.66
plotExpression	10.19	0.05	10.25
plotExprsFreqVsMean	2.00	0.03	2.03
plotExprsVsTxLength	2.58	0.03	2.61
plotFeatureData	1.02	0.01	1.03
plotHighestExprs	1.64	0.02	1.66
plotMDS	1.15	0.03	1.19
plotMetadata	0.24	0.00	0.23
plotPCA	6.37	0.05	6.42
plotPhenoData	0.69	0.01	0.71
plotPlatePosition	0.63	0.00	0.62
plotQC	3	0	3
plotRLE	7.14	0.30	7.44
plotReducedDim	4.59	0.05	4.64
plotScater	2.87	0.01	2.89
plotTSNE	3.33	0.02	3.34
read10XResults	0.52	0.00	0.52
readTxResults	0	0	0
rename	0.05	0.00	0.05
salmon-wrapper	0	0	0
scater_gui	0.17	0.01	0.19
summariseExprsAcrossFeatures	0.75	0.00	0.75
toSingleCellExperiment	0	0	0

name	user	system	elapsed
accessors	1.93	0.00	1.94
areSizeFactorsCentred	0.22	0.02	0.24
arrange	0.14	0.00	0.14
bootstraps	0.11	0.01	0.12
calcAverage	0.07	0.02	0.07
calcIsExprs	0.07	0.01	0.10
calculateCPM	0.07	0.04	0.09
calculateFPKM	0.09	0.01	0.11
calculateQCMetrics	0.66	0.05	0.70
calculateTPM	0.68	0.01	0.71
deprecated	0	0	0
downsampleCounts	0.32	0.04	0.34
filter	0.15	0.00	0.16
findImportantPCs	3.24	0.01	3.25
getBMFeatureAnnos	0	0	0
isOutlier	0.17	0.00	0.18
kallisto-wrapper	0	0	0
multiplot	3.21	0.02	3.21
mutate	0.07	0.01	0.08
newSCESet	0.03	0.02	0.04
nexprs	0.06	0.00	0.07
normaliseExprs	0.39	0.04	0.43
normalize	0.30	0.02	0.32
plotDiffusionMap	0.23	0.02	0.25
plotExplanatoryVariables	1.41	0.03	1.43
plotExpression	11.28	0.04	11.33
plotExprsFreqVsMean	2.33	0.04	2.36
plotExprsVsTxLength	3.06	0.01	3.08
plotFeatureData	0.59	0.03	0.63
plotHighestExprs	1.90	0.00	1.89
plotMDS	1.37	0.02	1.40
plotMetadata	0.25	0.00	0.25
plotPCA	6.17	0.00	6.18
plotPhenoData	0.85	0.00	0.84
plotPlatePosition	0.67	0.03	0.70
plotQC	2.45	0.01	2.47
plotRLE	5.61	0.25	5.86
plotReducedDim	4.23	0.05	4.28
plotScater	3.36	0.05	3.41
plotTSNE	2.41	0.03	3.79
read10XResults	0.34	0.00	0.35
readTxResults	0	0	0
rename	0.04	0.02	0.05
salmon-wrapper	0	0	0
scater_gui	0.23	0.00	0.23
summariseExprsAcrossFeatures	0.67	0.06	0.73
toSingleCellExperiment	0	0	0

CHECK report for scater on tokay1

Summary

Command output

Installation output

Tests output

Example timings