Multiple platform build/check report for BioC 3.13 - CHECK results for BASiCS on tokay2

Package: BASiCS

Version: 2.4.0

Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BASiCS.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings BASiCS_2.4.0.tar.gz

StartedAt: 2021-10-14 19:52:04 -0400 (Thu, 14 Oct 2021)

EndedAt: 2021-10-14 20:10:09 -0400 (Thu, 14 Oct 2021)

EllapsedTime: 1085.0 seconds

RetCode: 0

Status: OK

CheckDir: BASiCS.Rcheck

Warnings: 0

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BASiCS.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings BASiCS_2.4.0.tar.gz
###
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##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/BASiCS.Rcheck'
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'BASiCS/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'BASiCS' version '2.4.0'
* package encoding: UTF-8
* 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 'BASiCS' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   3.0Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* 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 LazyData ... 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 use of PKG_*FLAGS in Makefiles ... 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-3.13-bioc/R/library/BASiCS/libs/i386/BASiCS.dll':
  Found '_exit', possibly from '_exit' (C)
  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-3.13-bioc/R/library/BASiCS/libs/x64/BASiCS.dll':
  Found '_exit', possibly from '_exit' (C)
  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' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                        user system elapsed
BASiCS_MCMC             9.53   0.03    9.56
newBASiCS_Chain         6.53   0.25    6.79
BASiCS_TestDE           6.70   0.03    6.74
BASiCS_Chain            6.25   0.05    6.29
BASiCS_DenoisedCounts   5.69   0.05    5.74
BASiCS_DivideAndConquer 4.37   0.00   19.92
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                        user system elapsed
BASiCS_MCMC             9.79   0.11   10.02
newBASiCS_Chain         6.83   0.00    6.82
BASiCS_Chain            6.77   0.04    6.83
BASiCS_TestDE           6.29   0.04    6.32
BASiCS_DivideAndConquer 3.05   0.05   20.22
* 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 NOTEs
See
  'C:/Users/biocbuild/bbs-3.13-bioc/meat/BASiCS.Rcheck/00check.log'
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/BASiCS_2.4.0.tar.gz && rm -rf BASiCS.buildbin-libdir && mkdir BASiCS.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=BASiCS.buildbin-libdir BASiCS_2.4.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL BASiCS_2.4.0.zip && rm BASiCS_2.4.0.tar.gz BASiCS_2.4.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
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  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  4 2415k    4  100k    0     0   526k      0  0:00:04 --:--:--  0:00:04  527k
100 2415k  100 2415k    0     0  3375k      0 --:--:-- --:--:-- --:--:-- 3373k

install for i386

* installing *source* package 'BASiCS' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include'   -I"c:/extsoft/include"  -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c BASiCS.cpp -o BASiCS.o
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include'   -I"c:/extsoft/include"  -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
C:/rtools40/mingw32/bin/g++ -shared -s -static-libgcc -o BASiCS.dll tmp.def BASiCS.o RcppExports.o -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/i386 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/i386 -lRblas -lgfortran -lm -lquadmath -fopenmp -Lc:/extsoft/lib/i386 -Lc:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/BASiCS.buildbin-libdir/00LOCK-BASiCS/00new/BASiCS/libs/i386
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'BASiCS'
    finding HTML links ... done
    BASiCS-defunct                          html  
    BASiCS_Chain-methods                    html  
    BASiCS_Chain                            html  
    BASiCS_CorrectOffset                    html  
    BASiCS_DenoisedCounts                   html  
    finding level-2 HTML links ... done

    BASiCS_DenoisedRates                    html  
    BASiCS_DetectVG                         html  
    BASiCS_DiagHist                         html  
REDIRECT:topic	 Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.13-bioc/meat/BASiCS.buildbin-libdir/00LOCK-BASiCS/00new/BASiCS/help/BASiCS_diagHist.html
    BASiCS_DiagPlot                         html  
REDIRECT:topic	 Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.13-bioc/meat/BASiCS.buildbin-libdir/00LOCK-BASiCS/00new/BASiCS/help/BASiCS_diagPlot.html
    BASiCS_DivideAndConquer                 html  
    BASiCS_Draw                             html  
    BASiCS_EffectiveSize                    html  
REDIRECT:topic	 Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.13-bioc/meat/BASiCS.buildbin-libdir/00LOCK-BASiCS/00new/BASiCS/help/BASiCS_effectiveSize.html
    BASiCS_Filter                           html  
    BASiCS_LoadChain                        html  
    BASiCS_MCMC                             html  
    BASiCS_MockSCE                          html  
    BASiCS_PlotDE                           html  
    BASiCS_PlotOffset                       html  
    BASiCS_PlotVG                           html  
    BASiCS_PriorParam                       html  
    BASiCS_Result                           html  
    BASiCS_ResultDE                         html  
    BASiCS_ResultVG                         html  
    BASiCS_ResultsDE                        html  
    BASiCS_ShowFit                          html  
REDIRECT:topic	 Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.13-bioc/meat/BASiCS.buildbin-libdir/00LOCK-BASiCS/00new/BASiCS/help/BASiCS_showFit.html
    BASiCS_Sim                              html  
    BASiCS_Summary-methods                  html  
    BASiCS_Summary                          html  
    BASiCS_TestDE                           html  
    BASiCS_VarThresholdSearchHVG_LVG        html  
    BASiCS_VarianceDecomp                   html  
    ChainRNA                                html  
    ChainRNAReg                             html  
    ChainSC                                 html  
    ChainSCReg                              html  
    Summary-BASiCS_Chain-method             html  
    as.data.frame-methods                   html  
    dim-BASiCS_Chain-method                 html  
    dimnames-BASiCS_Chain-method            html  
    displayChainBASiCS-BASiCS_Chain-method
                                            html  
    displaySummaryBASiCS-BASiCS_Summary-method
                                            html  
    dot-generateSubsets                     html  
    format-methods                          html  
    makeExampleBASiCS_Data                  html  
    newBASiCS_Chain                         html  
    newBASiCS_Data                          html  
    plot-BASiCS_Chain-method                html  
    plot-BASiCS_Summary-method              html  
    rowData                                 html  
    show-BASiCS_ResultDE-method             html  
    show-BASiCS_ResultVG-method             html  
    show-BASiCS_ResultsDE-method            html  
    subset-BASiCS_Chain-method              html  
    subset-methods                          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 'BASiCS' ...
** libs
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include'   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c BASiCS.cpp -o BASiCS.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include'   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
C:/rtools40/mingw64/bin/g++ -shared -s -static-libgcc -o BASiCS.dll tmp.def BASiCS.o RcppExports.o -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/x64 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -fopenmp -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/BASiCS.buildbin-libdir/BASiCS/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'BASiCS' as BASiCS_2.4.0.zip
* DONE (BASiCS)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'BASiCS' successfully unpacked and MD5 sums checked


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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(BASiCS)
Loading required package: SingleCellExperiment
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'MatrixGenerics'

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

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

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.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    I, expand.grid, unname

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")'.


Attaching package: 'Biobase'

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

    rowMedians

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

    anyMissing, rowMedians

    Welcome to 'BASiCS'. If you used 'BASiCS' before its release in
    Bioconductor, please visit:
    https://github.com/catavallejos/BASiCS/wiki.
> 
> test_check("BASiCS")
== Skipped tests ===============================================================
* empty test (2)

[ FAIL 0 | WARN 1 | SKIP 2 | PASS 402 ]
> 
> proc.time()
   user  system elapsed 
 275.40    2.35  277.92


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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.

> library(testthat)
> library(BASiCS)
Loading required package: SingleCellExperiment
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'MatrixGenerics'

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

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

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.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    I, expand.grid, unname

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")'.


Attaching package: 'Biobase'

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

    rowMedians

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

    anyMissing, rowMedians

    Welcome to 'BASiCS'. If you used 'BASiCS' before its release in
    Bioconductor, please visit:
    https://github.com/catavallejos/BASiCS/wiki.
> 
> test_check("BASiCS")
== Skipped tests ===============================================================
* empty test (2)

[ FAIL 0 | WARN 1 | SKIP 2 | PASS 402 ]
> 
> proc.time()
   user  system elapsed 
 303.64    1.70  305.51

name	user	system	elapsed
BASiCS_Chain-methods	4.08	0.19	4.36
BASiCS_Chain	6.25	0.05	6.29
BASiCS_CorrectOffset	0.01	0.01	0.03
BASiCS_DenoisedCounts	5.69	0.05	5.74
BASiCS_DenoisedRates	4.22	0.00	4.21
BASiCS_DetectVG	0.73	0.11	0.85
BASiCS_DiagHist	1.08	0.01	1.09
BASiCS_DiagPlot	0.97	0.00	0.97
BASiCS_DivideAndConquer	4.37	0.00	19.92
BASiCS_Draw	0.93	0.02	0.94
BASiCS_EffectiveSize	0.39	0.00	0.39
BASiCS_Filter	0	0	0
BASiCS_LoadChain	3.33	0.00	3.33
BASiCS_MCMC	9.53	0.03	9.56
BASiCS_MockSCE	0.72	0.00	0.72
BASiCS_PlotDE	3.23	0.05	3.28
BASiCS_PlotOffset	0.82	0.00	0.82
BASiCS_PlotVG	0.33	0.00	0.33
BASiCS_PriorParam	0.56	0.00	0.57
BASiCS_ShowFit	0.24	0.00	0.23
BASiCS_Sim	1.69	0.00	1.69
BASiCS_Summary-methods	0.01	0.00	0.01
BASiCS_Summary	3.47	0.00	3.47
BASiCS_TestDE	6.70	0.03	6.74
BASiCS_VarThresholdSearchHVG_LVG	2.03	0.03	2.06
BASiCS_VarianceDecomp	0.18	0.00	0.18
Summary-BASiCS_Chain-method	0.06	0.00	0.06
dim-BASiCS_Chain-method	0.01	0.00	0.01
dimnames-BASiCS_Chain-method	0.02	0.01	0.04
displayChainBASiCS-BASiCS_Chain-method	0.31	0.08	1.76
displaySummaryBASiCS-BASiCS_Summary-method	0.25	0.01	0.27
makeExampleBASiCS_Data	0.69	0.00	0.68
newBASiCS_Chain	6.53	0.25	6.79
plot-BASiCS_Chain-method	0.17	0.02	0.18
plot-BASiCS_Summary-method	0.18	0.00	0.17
show-BASiCS_ResultDE-method	0.14	0.05	0.19
show-BASiCS_ResultVG-method	0.12	0.04	0.17
show-BASiCS_ResultsDE-method	0.13	0.05	0.18
subset-BASiCS_Chain-method	0.95	0.22	1.17

name	user	system	elapsed
BASiCS_Chain-methods	4.34	0.10	4.58
BASiCS_Chain	6.77	0.04	6.83
BASiCS_CorrectOffset	0.03	0.01	0.04
BASiCS_DenoisedCounts	4.42	0.02	4.44
BASiCS_DenoisedRates	3.90	0.03	4.05
BASiCS_DetectVG	0.90	0.01	0.90
BASiCS_DiagHist	1.18	0.00	1.19
BASiCS_DiagPlot	0.64	0.00	0.64
BASiCS_DivideAndConquer	3.05	0.05	20.22
BASiCS_Draw	1.00	0.03	1.03
BASiCS_EffectiveSize	0.25	0.00	0.25
BASiCS_Filter	0	0	0
BASiCS_LoadChain	3.82	0.02	3.84
BASiCS_MCMC	9.79	0.11	10.02
BASiCS_MockSCE	0.84	0.01	0.86
BASiCS_PlotDE	3.53	0.07	3.59
BASiCS_PlotOffset	1.31	0.01	1.44
BASiCS_PlotVG	0.41	0.02	0.42
BASiCS_PriorParam	0.64	0.00	0.64
BASiCS_ShowFit	0.25	0.03	0.28
BASiCS_Sim	1.48	0.01	1.50
BASiCS_Summary-methods	0.02	0.00	0.02
BASiCS_Summary	3.33	0.03	3.36
BASiCS_TestDE	6.29	0.04	6.32
BASiCS_VarThresholdSearchHVG_LVG	1.80	0.01	1.82
BASiCS_VarianceDecomp	0.17	0.02	0.18
Summary-BASiCS_Chain-method	0.07	0.00	0.07
dim-BASiCS_Chain-method	0	0	0
dimnames-BASiCS_Chain-method	0.01	0.00	0.01
displayChainBASiCS-BASiCS_Chain-method	0.14	0.03	0.17
displaySummaryBASiCS-BASiCS_Summary-method	0.16	0.01	0.18
makeExampleBASiCS_Data	0.61	0.00	0.61
newBASiCS_Chain	6.83	0.00	6.82
plot-BASiCS_Chain-method	0.17	0.00	0.18
plot-BASiCS_Summary-method	0.14	0.04	0.17
show-BASiCS_ResultDE-method	0.12	0.03	0.15
show-BASiCS_ResultVG-method	0.13	0.04	0.18
show-BASiCS_ResultsDE-method	0.14	0.02	0.15
subset-BASiCS_Chain-method	1.01	0.01	1.03

CHECK results for BASiCS on tokay2

Summary

Command output

Installation output

Tests output

Example timings