Multiple platform build/check report for BioC 3.20 - CHECK results for BASiCS on kunpeng2

Hostname	OS	Arch (*)	R version	Installed pkgs
teran2	Linux (Ubuntu 24.04.1 LTS)	x86_64	4.4.1 (2024-06-14) -- "Race for Your Life"	4445
palomino8	Windows Server 2022 Datacenter	x64	4.4.1 (2024-06-14 ucrt) -- "Race for Your Life"	4450
lconway	macOS 12.7.1 Monterey	x86_64	4.4.1 (2024-06-14) -- "Race for Your Life"	4483
kjohnson3	macOS 13.6.5 Ventura	arm64	4.4.1 (2024-06-14) -- "Race for Your Life"	4430
kunpeng2	Linux (openEuler 22.03 LTS-SP1)	aarch64	4.4.1 (2024-06-14) -- "Race for Your Life"	4428
Click on any hostname to see more info about the system (e.g. compilers) () as reported by 'uname -p', except on Windows and Mac OS X*

CHECK results for BASiCS on kunpeng2

To the developers/maintainers of the BASiCS package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BASiCS.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results

Summary

Package: BASiCS

Version: 2.17.0

Command: /home/biocbuild/R/R/bin/R CMD check --install=check:BASiCS.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings BASiCS_2.17.0.tar.gz

StartedAt: 2024-09-17 02:44:57 -0000 (Tue, 17 Sep 2024)

EndedAt: 2024-09-17 02:57:46 -0000 (Tue, 17 Sep 2024)

EllapsedTime: 769.3 seconds

RetCode: 0

Status: OK

CheckDir: BASiCS.Rcheck

Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:BASiCS.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings BASiCS_2.17.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/BASiCS.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14)
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BASiCS/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BASiCS’ version ‘2.17.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘BASiCS’ can be installed ... OK
* used C++ compiler: ‘g++ (GCC) 10.3.1’
* checking C++ specification ... NOTE
  Specified C++11: please drop specification unless essential
* checking installed package size ... NOTE
  installed size is 13.9Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs  11.0Mb
* 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 code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... 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 use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                          user system elapsed
BASiCS_MCMC             10.342  0.355  10.717
BASiCS_TestDE            9.543  0.147   9.708
newBASiCS_Chain          6.014  0.128   6.153
BASiCS_Chain             5.481  0.196   5.692
BASiCS_DivideAndConquer  4.084  0.161  22.538
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/BASiCS.Rcheck/00check.log’
for details.

Installation output

BASiCS.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL BASiCS
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.4.1/site-library’
* installing *source* package ‘BASiCS’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (GCC) 10.3.1’
using C++11
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-library/RcppArmadillo/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall  -c BASiCS.cpp -o BASiCS.o
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-library/RcppArmadillo/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -shared -L/home/biocbuild/R/R-4.4.1/lib -L/usr/local/lib -o BASiCS.so BASiCS.o RcppExports.o -lopenblas -L/usr/lib/gcc/aarch64-linux-gnu/10.3.1 -lgfortran -lm -fopenmp -L/home/biocbuild/R/R-4.4.1/lib -lR
installing to /home/biocbuild/R/R-4.4.1/site-library/00LOCK-BASiCS/00new/BASiCS/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (BASiCS)

Tests output

BASiCS.Rcheck/tests/testthat.Rout


R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu

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

Attaching package: 'BiocGenerics'

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, aperm, 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, table, tapply,
    union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    findMatches

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

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor

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


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")
-------------------------------------------------------------
Log-fold change thresholds are now set in a log2 scale. 
Original BASiCS release used a natural logarithm scale.
-------------------------------------------------------------
Offset estimate: 0.6714
(ratio SC vs P&S).
-------------------------------------------------------------

-------------------------------------------------------------
Log-fold change thresholds are now set in a log2 scale. 
Original BASiCS release used a natural logarithm scale.
-------------------------------------------------------------
Offset estimate: 0.6714
(ratio SC vs P&S).
To visualise its effect, please use 'PlotOffset = TRUE'.
-------------------------------------------------------------

-------------------------------------------------------------
Log-fold change thresholds are now set in a log2 scale. 
Original BASiCS release used a natural logarithm scale.
-------------------------------------------------------------
Offset estimate: 0.6714
(ratio Group1 vs Group2).
To visualise its effect, please use 'PlotOffset = TRUE'.
-------------------------------------------------------------

For Differential mean task:
the posterior probability threshold chosen via EFDR calibration is too low.
Probability threshold automatically set equal to 'ProbThresholdM'.
EFDR calibration failed for Differential dispersion task. 
Probability threshold automatically set equal to 'ProbThresholdD'.
-------------------------------------------------------------
Log-fold change thresholds are now set in a log2 scale. 
Original BASiCS release used a natural logarithm scale.
-------------------------------------------------------------
Offset estimate: 0.6714
(ratio SC vs P&S).
To visualise its effect, please use 'PlotOffset = TRUE'.
-------------------------------------------------------------

-------------------------------------------------------------
Log-fold change thresholds are now set in a log2 scale. 
Original BASiCS release used a natural logarithm scale.
-------------------------------------------------------------
Offset estimate: 0.6714
(ratio Group1 vs Group2).
-------------------------------------------------------------

For Differential mean task:
the posterior probability threshold chosen via EFDR calibration is too low.
Probability threshold automatically set equal to 'ProbThresholdM'.
EFDR calibration failed for Differential dispersion task. 
Probability threshold automatically set equal to 'ProbThresholdD'.
-------------------------------------------------------------
Log-fold change thresholds are now set in a log2 scale. 
Original BASiCS release used a natural logarithm scale.
-------------------------------------------------------------
Offset estimate: 0.6714
(ratio SC vs P&S).
To visualise its effect, please use 'PlotOffset = TRUE'.
-------------------------------------------------------------

-------------------------------------------------------------
Log-fold change thresholds are now set in a log2 scale. 
Original BASiCS release used a natural logarithm scale.
-------------------------------------------------------------
Offset estimate: 0.6714
(ratio SC vs P&S).
To visualise its effect, please use 'PlotOffset = TRUE'.
-------------------------------------------------------------

-------------------------------------------------------------
Log-fold change thresholds are now set in a log2 scale. 
Original BASiCS release used a natural logarithm scale.
-------------------------------------------------------------
Offset estimate: 0.6787
(ratio SC vs P&S).
To visualise its effect, please use 'PlotOffset = TRUE'.
-------------------------------------------------------------

-------------------------------------------------------------
Log-fold change thresholds are now set in a log2 scale. 
Original BASiCS release used a natural logarithm scale.
-------------------------------------------------------------
Log-fold change thresholds are now set in a log2 scale. 
Original BASiCS release used a natural logarithm scale.
-------------------------------------------------------------
Offset estimate: 0.6787
(ratio Group1 vs Group2).
To visualise its effect, please use 'PlotOffset = TRUE'.
-------------------------------------------------------------

-------------------------------------------------------------
Log-fold change thresholds are now set in a log2 scale. 
Original BASiCS release used a natural logarithm scale.
-------------------------------------------------------------
Offset estimate: 0.6787
(ratio Group1 vs Group2).
To visualise its effect, please use 'PlotOffset = TRUE'.
-------------------------------------------------------------

EFDR calibration failed for Differential mean task. 
Probability threshold automatically set equal to 'ProbThresholdM'.
EFDR calibration failed for Differential dispersion task. 
Probability threshold automatically set equal to 'ProbThresholdD'.
For Differential residual dispersion task:
the posterior probability threshold chosen via EFDR calibration is too low.
Probability threshold automatically set equal to 'ProbThresholdR'.
-------------------------------------------------------------
Log-fold change thresholds are now set in a log2 scale. 
Original BASiCS release used a natural logarithm scale.
-------------------------------------------------------------
Offset estimate: 0.6787
(ratio SC vs P&S).
To visualise its effect, please use 'PlotOffset = TRUE'.
-------------------------------------------------------------

-------------------------------------------------------------
Log-fold change thresholds are now set in a log2 scale. 
Original BASiCS release used a natural logarithm scale.
-------------------------------------------------------------
Offset estimate: 0.6787
(ratio Group1 vs Group2).
To visualise its effect, please use 'PlotOffset = TRUE'.
-------------------------------------------------------------

EFDR calibration failed for Differential mean task. 
Probability threshold automatically set equal to 'ProbThresholdM'.
EFDR calibration failed for Differential dispersion task. 
Probability threshold automatically set equal to 'ProbThresholdD'.
For Differential residual dispersion task:
the posterior probability threshold chosen via EFDR calibration is too low.
Probability threshold automatically set equal to 'ProbThresholdR'.
altExp 'spike-ins' is assumed to contain spike-in genes.
see help(altExp) for details. 

Running with spikes BASiCS sampler (regression case) ... 

-------------------------------------------------------------
MCMC running time 
-------------------------------------------------------------
user: 0.013
system: 0
elapsed: 0.013

-------------------------------------------------------------
Output 
-------------------------------------------------------------

-------------------------------------------------------------
BASiCS version 2.17.0 : 
vertical integration (spikes case) 
-------------------------------------------------------------

altExp 'spike-ins' is assumed to contain spike-in genes.
see help(altExp) for details. 

Running with spikes BASiCS sampler (regression case) ... 

-------------------------------------------------------------
MCMC running time 
-------------------------------------------------------------
user: 0.011
system: 0
elapsed: 0.012

-------------------------------------------------------------
Output 
-------------------------------------------------------------

-------------------------------------------------------------
BASiCS version 2.17.0 : 
vertical integration (spikes case) 
-------------------------------------------------------------

altExp 'spike-ins' is assumed to contain spike-in genes.
see help(altExp) for details. 

altExp 'spike-ins' is assumed to contain spike-in genes.
see help(altExp) for details. 

Running with spikes BASiCS sampler (regression case) ... 

-------------------------------------------------------------
MCMC running time 
-------------------------------------------------------------
user: 0.013
system: 0
elapsed: 0.012

-------------------------------------------------------------
Output 
-------------------------------------------------------------

-------------------------------------------------------------
BASiCS version 2.17.0 : 
vertical integration (spikes case) 
-------------------------------------------------------------

altExp 'spike-ins' is assumed to contain spike-in genes.
see help(altExp) for details. 

Running with spikes BASiCS sampler (regression case) ... 

-------------------------------------------------------------
MCMC running time 
-------------------------------------------------------------
user: 0.012
system: 0
elapsed: 0.012

-------------------------------------------------------------
Output 
-------------------------------------------------------------

-------------------------------------------------------------
BASiCS version 2.17.0 : 
vertical integration (spikes case) 
-------------------------------------------------------------

Combining batch posteriors for mu
Combining batch posteriors for delta
Combining batch posteriors for phi
Combining batch posteriors for s
Combining batch posteriors for nu
Combining batch posteriors for theta
Combining batch posteriors for beta
Combining batch posteriors for sigma2
Combining batch posteriors for epsilon
Combining batch posteriors for RBFLocations
altExp 'spike-ins' is assumed to contain spike-in genes.
see help(altExp) for details. 

altExp 'spike-ins' is assumed to contain spike-in genes.
see help(altExp) for details. 

-------------------------------------------------------------
NOTE: default choice PriorDelta = 'log-normal'  (recommended value). 
Vallejos et al (2015) used a 'gamma' prior instead.
-------------------------------------------------------------

Running with spikes BASiCS sampler (no regression) ... 

-------------------------------------------------------------
MCMC running time 
-------------------------------------------------------------
user: 0.012
system: 0
elapsed: 0.012

-------------------------------------------------------------
Output 
-------------------------------------------------------------

-------------------------------------------------------------
BASiCS version 2.17.0 : 
vertical integration (spikes case) 
-------------------------------------------------------------

altExp 'spike-ins' is assumed to contain spike-in genes.
see help(altExp) for details. 

-------------------------------------------------------------
NOTE: default choice PriorDelta = 'log-normal'  (recommended value). 
Vallejos et al (2015) used a 'gamma' prior instead.
-------------------------------------------------------------

Running with spikes BASiCS sampler (no regression) ... 

-------------------------------------------------------------
MCMC running time 
-------------------------------------------------------------
user: 0.01
system: 0
elapsed: 0.01

-------------------------------------------------------------
Output 
-------------------------------------------------------------

-------------------------------------------------------------
BASiCS version 2.17.0 : 
vertical integration (spikes case) 
-------------------------------------------------------------

Combining batch posteriors for mu
Combining batch posteriors for delta
Combining batch posteriors for phi
Combining batch posteriors for s
Combining batch posteriors for nu
Combining batch posteriors for theta
Running no spikes BASiCS sampler (regression case) ... 

-------------------------------------------------------------
MCMC running time 
-------------------------------------------------------------
user: 0.012
system: 0
elapsed: 0.012

-------------------------------------------------------------
Output 
-------------------------------------------------------------

Running no spikes BASiCS sampler (regression case) ... 

-------------------------------------------------------------
MCMC running time 
-------------------------------------------------------------
user: 0.011
system: 0
elapsed: 0.011

-------------------------------------------------------------
Output 
-------------------------------------------------------------

Combining batch posteriors for mu
Combining batch posteriors for delta
Combining batch posteriors for s
Combining batch posteriors for nu
Combining batch posteriors for theta
Combining batch posteriors for beta
Combining batch posteriors for sigma2
Combining batch posteriors for epsilon
Combining batch posteriors for RBFLocations
-------------------------------------------------------------
NOTE: default choice PriorDelta = 'log-normal'  (recommended value). 
Vallejos et al (2015) used a 'gamma' prior instead.
-------------------------------------------------------------

Running no spikes BASiCS sampler (no regression) ... 

-------------------------------------------------------------
MCMC running time 
-------------------------------------------------------------
user: 0.01
system: 0
elapsed: 0.01

-------------------------------------------------------------
Output 
-------------------------------------------------------------

-------------------------------------------------------------
NOTE: default choice PriorDelta = 'log-normal'  (recommended value). 
Vallejos et al (2015) used a 'gamma' prior instead.
-------------------------------------------------------------

Running no spikes BASiCS sampler (no regression) ... 

-------------------------------------------------------------
MCMC running time 
-------------------------------------------------------------
user: 0.01
system: 0
elapsed: 0.01

-------------------------------------------------------------
Output 
-------------------------------------------------------------

Combining batch posteriors for mu
Combining batch posteriors for delta
Combining batch posteriors for s
Combining batch posteriors for nu
Combining batch posteriors for theta
altExp 'spike-ins' is assumed to contain spike-in genes.
see help(altExp) for details. 

altExp 'spike-ins' is assumed to contain spike-in genes.
see help(altExp) for details. 

Running with spikes BASiCS sampler (regression case) ... 

-------------------------------------------------------------
MCMC running time 
-------------------------------------------------------------
user: 0.014
system: 0
elapsed: 0.014

-------------------------------------------------------------
Output 
-------------------------------------------------------------

-------------------------------------------------------------
BASiCS version 2.17.0 : 
vertical integration (spikes case) 
-------------------------------------------------------------

altExp 'spike-ins' is assumed to contain spike-in genes.
see help(altExp) for details. 

Running with spikes BASiCS sampler (regression case) ... 

-------------------------------------------------------------
MCMC running time 
-------------------------------------------------------------
user: 0.011
system: 0
elapsed: 0.01

-------------------------------------------------------------
Output 
-------------------------------------------------------------

-------------------------------------------------------------
BASiCS version 2.17.0 : 
vertical integration (spikes case) 
-------------------------------------------------------------

Combining batch posteriors for mu
Combining batch posteriors for delta
Combining batch posteriors for phi
Combining batch posteriors for s
Combining batch posteriors for nu
Combining batch posteriors for theta
Combining batch posteriors for beta
Combining batch posteriors for sigma2
Combining batch posteriors for epsilon
Combining batch posteriors for RBFLocations
altExp 'spike-ins' is assumed to contain spike-in genes.
see help(altExp) for details. 

altExp 'spike-ins' is assumed to contain spike-in genes.
see help(altExp) for details. 

-------------------------------------------------------------
NOTE: default choice PriorDelta = 'log-normal'  (recommended value). 
Vallejos et al (2015) used a 'gamma' prior instead.
-------------------------------------------------------------

Running with spikes BASiCS sampler (no regression) ... 

-------------------------------------------------------------
MCMC running time 
-------------------------------------------------------------
user: 0.012
system: 0
elapsed: 0.011

-------------------------------------------------------------
Output 
-------------------------------------------------------------

-------------------------------------------------------------
BASiCS version 2.17.0 : 
vertical integration (spikes case) 
-------------------------------------------------------------

altExp 'spike-ins' is assumed to contain spike-in genes.
see help(altExp) for details. 

-------------------------------------------------------------
NOTE: default choice PriorDelta = 'log-normal'  (recommended value). 
Vallejos et al (2015) used a 'gamma' prior instead.
-------------------------------------------------------------

Running with spikes BASiCS sampler (no regression) ... 

-------------------------------------------------------------
MCMC running time 
-------------------------------------------------------------
user: 0.011
system: 0
elapsed: 0.011

-------------------------------------------------------------
Output 
-------------------------------------------------------------

-------------------------------------------------------------
BASiCS version 2.17.0 : 
vertical integration (spikes case) 
-------------------------------------------------------------

Combining batch posteriors for mu
Combining batch posteriors for delta
Combining batch posteriors for phi
Combining batch posteriors for s
Combining batch posteriors for nu
Combining batch posteriors for theta
Running no spikes BASiCS sampler (regression case) ... 

-------------------------------------------------------------
MCMC running time 
-------------------------------------------------------------
user: 0.013
system: 0
elapsed: 0.013

-------------------------------------------------------------
Output 
-------------------------------------------------------------

Running no spikes BASiCS sampler (regression case) ... 

-------------------------------------------------------------
MCMC running time 
-------------------------------------------------------------
user: 0.01
system: 0
elapsed: 0.01

-------------------------------------------------------------
Output 
-------------------------------------------------------------

Combining batch posteriors for mu
Combining batch posteriors for delta
Combining batch posteriors for s
Combining batch posteriors for nu
Combining batch posteriors for theta
Combining batch posteriors for beta
Combining batch posteriors for sigma2
Combining batch posteriors for epsilon
Combining batch posteriors for RBFLocations
-------------------------------------------------------------
NOTE: default choice PriorDelta = 'log-normal'  (recommended value). 
Vallejos et al (2015) used a 'gamma' prior instead.
-------------------------------------------------------------

Running no spikes BASiCS sampler (no regression) ... 

-------------------------------------------------------------
MCMC running time 
-------------------------------------------------------------
user: 0.009
system: 0
elapsed: 0.01

-------------------------------------------------------------
Output 
-------------------------------------------------------------

-------------------------------------------------------------
NOTE: default choice PriorDelta = 'log-normal'  (recommended value). 
Vallejos et al (2015) used a 'gamma' prior instead.
-------------------------------------------------------------

Running no spikes BASiCS sampler (no regression) ... 

-------------------------------------------------------------
MCMC running time 
-------------------------------------------------------------
user: 0.01
system: 0
elapsed: 0.01

-------------------------------------------------------------
Output 
-------------------------------------------------------------

Combining batch posteriors for mu
Combining batch posteriors for delta
Combining batch posteriors for s
Combining batch posteriors for nu
Combining batch posteriors for theta
-------------------------------------------------------------
NOTE: default choice PriorDelta = 'log-normal'  (recommended value). 
Vallejos et al (2015) used a 'gamma' prior instead.
-------------------------------------------------------------

Running no spikes BASiCS sampler (no regression) ... 

-------------------------------------------------------------
MCMC running time 
-------------------------------------------------------------
user: 0.016
system: 0
elapsed: 0.017

-------------------------------------------------------------
Output 
-------------------------------------------------------------

altExp 'spike-ins' is assumed to contain spike-in genes.
see help(altExp) for details. 

Running with spikes BASiCS sampler (regression case) ... 

-------------------------------------------------------------
MCMC running time 
-------------------------------------------------------------
user: 0.065
system: 0
elapsed: 0.065

-------------------------------------------------------------
Output 
-------------------------------------------------------------

-------------------------------------------------------------
BASiCS version 2.17.0 : 
vertical integration (spikes case) 
-------------------------------------------------------------

altExp 'spike-ins' is assumed to contain spike-in genes.
see help(altExp) for details. 

Running with spikes BASiCS sampler (regression case) ... 

-------------------------------------------------------------
MCMC running time 
-------------------------------------------------------------
user: 0.067
system: 0
elapsed: 0.066

-------------------------------------------------------------
Output 
-------------------------------------------------------------

-------------------------------------------------------------
BASiCS version 2.17.0 : 
vertical integration (spikes case) 
-------------------------------------------------------------

Combining batch posteriors for mu
Combining batch posteriors for delta
Combining batch posteriors for phi
Combining batch posteriors for s
Combining batch posteriors for nu
Combining batch posteriors for theta
Combining batch posteriors for beta
Combining batch posteriors for sigma2
Combining batch posteriors for epsilon
Combining batch posteriors for RBFLocations
Combining batch posteriors for mu
Combining batch posteriors for delta
Combining batch posteriors for phi
Combining batch posteriors for s
Combining batch posteriors for nu
Combining batch posteriors for theta
Combining batch posteriors for beta
Combining batch posteriors for sigma2
Combining batch posteriors for epsilon
Combining batch posteriors for RBFLocations
Combining batch posteriors for mu
Combining batch posteriors for mu
Combining batch posteriors for delta
Combining batch posteriors for phi
Combining batch posteriors for s
Combining batch posteriors for nu
Combining batch posteriors for theta
Cannot find a balanced split with 9 quantiles, trying again with 8
altExp 'spike-ins' is assumed to contain spike-in genes.
see help(altExp) for details. 

Running with spikes BASiCS sampler (regression case) ... 

-------------------------------------------------------------
MCMC running time 
-------------------------------------------------------------
user: 0.07
system: 0
elapsed: 0.071

-------------------------------------------------------------
Output 
-------------------------------------------------------------

-------------------------------------------------------------
BASiCS version 2.17.0 : 
vertical integration (spikes case) 
-------------------------------------------------------------

altExp 'spike-ins' is assumed to contain spike-in genes.
see help(altExp) for details. 

Running with spikes BASiCS sampler (regression case) ... 

-------------------------------------------------------------
MCMC running time 
-------------------------------------------------------------
user: 0.06
system: 0
elapsed: 0.06

-------------------------------------------------------------
Output 
-------------------------------------------------------------

-------------------------------------------------------------
BASiCS version 2.17.0 : 
vertical integration (spikes case) 
-------------------------------------------------------------

Generating partitions...
Starting MCMC...
-------------------------------------------------------------
NOTE: default choice PriorDelta = 'log-normal'  (recommended value). 
Vallejos et al (2015) used a 'gamma' prior instead.
-------------------------------------------------------------

Running no spikes BASiCS sampler (no regression) ... 

-----------------------------------------------------
MCMC sampler has been started: 200 iterations to go.
-----------------------------------------------------
RefGene: 39
RefGene: 0
RefGene: 11
RefGene: 0
RefGene: 16
RefGene: 16
RefGene: 0
RefGene: 44
RefGene: 39
RefGene: 17
RefGene: 43
RefGene: 13
RefGene: 16
RefGene: 16
RefGene: 16
RefGene: 0
RefGene: 43
RefGene: 13
RefGene: 13
RefGene: 17
RefGene: 13
RefGene: 16
RefGene: 13
RefGene: 43
RefGene: 17
RefGene: 43
RefGene: 43
RefGene: 16
RefGene: 44
RefGene: 43
RefGene: 15
RefGene: 13
RefGene: 0
RefGene: 43
RefGene: 13
RefGene: 43
RefGene: 16
RefGene: 13
RefGene: 43
RefGene: 17
RefGene: 16
RefGene: 39
RefGene: 43
RefGene: 11
RefGene: 43
RefGene: 44
RefGene: 39
RefGene: 31
RefGene: 15
RefGene: 0
RefGene: 17
RefGene: 31
RefGene: 13
RefGene: 16
RefGene: 43
RefGene: 44
RefGene: 44
RefGene: 39
RefGene: 17
RefGene: 13
RefGene: 44
RefGene: 44
RefGene: 31
RefGene: 15
RefGene: 43
RefGene: 11
RefGene: 11
RefGene: 44
RefGene: 31
RefGene: 13
RefGene: 0
RefGene: 11
RefGene: 0
RefGene: 44
RefGene: 44
RefGene: 16
RefGene: 44
RefGene: 15
RefGene: 16
RefGene: 15
RefGene: 0
RefGene: 31
RefGene: 39
RefGene: 16
RefGene: 16
RefGene: 13
RefGene: 13
RefGene: 11
RefGene: 15
RefGene: 17
RefGene: 43
RefGene: 31
RefGene: 0
RefGene: 15
RefGene: 15
RefGene: 0
RefGene: 13
RefGene: 17
RefGene: 44
RefGene: 0
-----------------------------------------------------
End of Burn-in period.
-----------------------------------------------------
RefGene: 17
RefGene: 39
RefGene: 11
RefGene: 43
RefGene: 16
RefGene: 44
RefGene: 0
RefGene: 13
RefGene: 16
RefGene: 11
RefGene: 44
RefGene: 17
RefGene: 44
RefGene: 44
RefGene: 31
RefGene: 16
RefGene: 13
RefGene: 17
RefGene: 44
RefGene: 43
RefGene: 0
RefGene: 17
RefGene: 31
RefGene: 39
RefGene: 39
RefGene: 16
RefGene: 17
RefGene: 17
RefGene: 16
RefGene: 17
RefGene: 39
RefGene: 0
RefGene: 13
RefGene: 31
RefGene: 11
RefGene: 11
RefGene: 44
RefGene: 17
RefGene: 0
RefGene: 39
RefGene: 15
RefGene: 31
RefGene: 15
RefGene: 17
RefGene: 11
RefGene: 39
RefGene: 17
RefGene: 39
RefGene: 0
RefGene: 43
RefGene: 31
RefGene: 31
RefGene: 43
RefGene: 31
RefGene: 31
RefGene: 16
RefGene: 13
RefGene: 11
RefGene: 11
RefGene: 16
RefGene: 16
RefGene: 11
RefGene: 43
RefGene: 11
RefGene: 44
RefGene: 31
RefGene: 31
RefGene: 31
RefGene: 15
RefGene: 17
RefGene: 11
RefGene: 0
RefGene: 0
RefGene: 13
RefGene: 44
RefGene: 16
RefGene: 39
RefGene: 15
RefGene: 15
RefGene: 11
RefGene: 0
RefGene: 13
RefGene: 31
RefGene: 16
RefGene: 15
RefGene: 43
RefGene: 31
RefGene: 15
RefGene: 39
RefGene: 44
RefGene: 0
RefGene: 13
RefGene: 43
RefGene: 16
RefGene: 16
RefGene: 39
RefGene: 0
RefGene: 17
RefGene: 39
RefGene: 43
 
-----------------------------------------------------
-----------------------------------------------------
All 200 MCMC iterations have been completed.
-----------------------------------------------------
-----------------------------------------------------
 
-----------------------------------------------------
Please see below a summary of the overall acceptance rates.
-----------------------------------------------------
 
Minimum acceptance rate among mu[i]'s: 0.16
Average acceptance rate among mu[i]'s: 0.4956
Maximum acceptance rate among mu[i]'s: 0.82
 
 
Minimum acceptance rate among delta[i]'s: 0.53
Average acceptance rate among delta[i]'s: 0.665
Maximum acceptance rate among delta[i]'s: 0.83
 
 
Minimum acceptance rate among nu[jk]'s: 0.87
Average acceptance rate among nu[jk]'s: 0.9546
Maximum acceptance rate among nu[jk]'s: 1
 
 
Minimum acceptance rate among theta[k]'s: 0.28
Average acceptance rate among theta[k]'s: 0.64
Maximum acceptance rate among theta[k]'s: 1
 
-----------------------------------------------------
 
-------------------------------------------------------------
MCMC running time 
-------------------------------------------------------------
user: 0.206
system: 0
elapsed: 0.206

-------------------------------------------------------------
Output 
-------------------------------------------------------------


-------------------------------------------------------------
NOTE: default choice PriorDelta = 'log-normal'  (recommended value). 
Vallejos et al (2015) used a 'gamma' prior instead.
-------------------------------------------------------------

Running no spikes BASiCS sampler (no regression) ... 

-----------------------------------------------------
MCMC sampler has been started: 200 iterations to go.
-----------------------------------------------------
RefGene: 10
RefGene: 10
RefGene: 19
RefGene: 22
RefGene: 23
RefGene: 14
RefGene: 10
RefGene: 23
RefGene: 36
RefGene: 10
RefGene: 36
RefGene: 49
RefGene: 36
RefGene: 14
RefGene: 9
RefGene: 10
RefGene: 10
RefGene: 14
RefGene: 49
RefGene: 22
RefGene: 23
RefGene: 10
RefGene: 23
RefGene: 22
RefGene: 14
RefGene: 22
RefGene: 9
RefGene: 10
RefGene: 10
RefGene: 9
RefGene: 22
RefGene: 19
RefGene: 23
RefGene: 23
RefGene: 36
RefGene: 19
RefGene: 47
RefGene: 22
RefGene: 14
RefGene: 11
RefGene: 22
RefGene: 22
RefGene: 19
RefGene: 22
RefGene: 19
RefGene: 9
RefGene: 9
RefGene: 22
RefGene: 47
RefGene: 36
RefGene: 11
RefGene: 49
RefGene: 36
RefGene: 14
RefGene: 14
RefGene: 10
RefGene: 10
RefGene: 10
RefGene: 22
RefGene: 36
RefGene: 22
RefGene: 11
RefGene: 14
RefGene: 23
RefGene: 10
RefGene: 11
RefGene: 36
RefGene: 36
RefGene: 23
RefGene: 14
RefGene: 14
RefGene: 22
RefGene: 49
RefGene: 11
RefGene: 14
RefGene: 11
RefGene: 49
RefGene: 9
RefGene: 19
RefGene: 9
RefGene: 11
RefGene: 9
RefGene: 49
RefGene: 11
RefGene: 36
RefGene: 22
RefGene: 10
RefGene: 14
RefGene: 49
RefGene: 22
RefGene: 22
RefGene: 47
RefGene: 11
RefGene: 36
RefGene: 9
RefGene: 22
RefGene: 47
RefGene: 10
RefGene: 23
RefGene: 19
-----------------------------------------------------
End of Burn-in period.
-----------------------------------------------------
RefGene: 23
RefGene: 23
RefGene: 11
RefGene: 49
RefGene: 23
RefGene: 14
RefGene: 47
RefGene: 49
RefGene: 19
RefGene: 10
RefGene: 11
RefGene: 36
RefGene: 9
RefGene: 47
RefGene: 23
RefGene: 14
RefGene: 9
RefGene: 14
RefGene: 22
RefGene: 11
RefGene: 49
RefGene: 49
RefGene: 10
RefGene: 47
RefGene: 22
RefGene: 11
RefGene: 14
RefGene: 23
RefGene: 9
RefGene: 10
RefGene: 23
RefGene: 22
RefGene: 14
RefGene: 9
RefGene: 22
RefGene: 23
RefGene: 10
RefGene: 9
RefGene: 22
RefGene: 9
RefGene: 47
RefGene: 47
RefGene: 11
RefGene: 9
RefGene: 49
RefGene: 9
RefGene: 49
RefGene: 23
RefGene: 36
RefGene: 10
RefGene: 11
RefGene: 47
RefGene: 49
RefGene: 10
RefGene: 10
RefGene: 23
RefGene: 23
RefGene: 11
RefGene: 14
RefGene: 11
RefGene: 11
RefGene: 49
RefGene: 10
RefGene: 49
RefGene: 22
RefGene: 14
RefGene: 9
RefGene: 36
RefGene: 49
RefGene: 22
RefGene: 10
RefGene: 23
RefGene: 23
RefGene: 23
RefGene: 22
RefGene: 23
RefGene: 19
RefGene: 9
RefGene: 36
RefGene: 22
RefGene: 10
RefGene: 47
RefGene: 36
RefGene: 23
RefGene: 11
RefGene: 47
RefGene: 47
RefGene: 10
RefGene: 49
RefGene: 49
RefGene: 36
RefGene: 49
RefGene: 36
RefGene: 11
RefGene: 11
RefGene: 11
RefGene: 11
RefGene: 23
RefGene: 10
RefGene: 10
 
-----------------------------------------------------
-----------------------------------------------------
All 200 MCMC iterations have been completed.
-----------------------------------------------------
-----------------------------------------------------
 
-----------------------------------------------------
Please see below a summary of the overall acceptance rates.
-----------------------------------------------------
 
Minimum acceptance rate among mu[i]'s: 0.18
Average acceptance rate among mu[i]'s: 0.5054
Maximum acceptance rate among mu[i]'s: 0.76
 
 
Minimum acceptance rate among delta[i]'s: 0.52
Average acceptance rate among delta[i]'s: 0.6832
Maximum acceptance rate among delta[i]'s: 0.82
 
 
Minimum acceptance rate among nu[jk]'s: 0.84
Average acceptance rate among nu[jk]'s: 0.9584
Maximum acceptance rate among nu[jk]'s: 1
 
 
Minimum acceptance rate among theta[k]'s: 0.04
Average acceptance rate among theta[k]'s: 0.375
Maximum acceptance rate among theta[k]'s: 0.71
 
-----------------------------------------------------
 
-------------------------------------------------------------
MCMC running time 
-------------------------------------------------------------
user: 0.208
system: 0
elapsed: 0.211

-------------------------------------------------------------
Output 
-------------------------------------------------------------


Combining batch posteriors for mu
Combining batch posteriors for delta
Combining batch posteriors for s

Combining batch posteriors for nu
Combining batch posteriors for theta

sumAux (line 117): 146.424
sumAux (line 117): 136.459
For LVG detection task:
the posterior probability threshold chosen via EFDR calibration is too low.
Probability threshold automatically set equal to 'ProbThreshold'.
For LVG detection task:
the posterior probability threshold chosen via EFDR calibration is too low.
Probability threshold automatically set equal to 'ProbThreshold'.
For LVG detection task:
the posterior probability threshold chosen via EFDR calibration is too low.
Probability threshold automatically set equal to 'ProbThreshold'.
Evaluating variance contribution threshold = 25 % ... 

Evaluating variance contribution threshold = 50 % ... 

Evaluating variance contribution threshold = 75 % ... 

Evaluating variance contribution threshold = 25 % ... 

Evaluating variance contribution threshold = 50 % ... 

Evaluating variance contribution threshold = 75 % ... 

For LVG detection task:
the posterior probability threshold chosen via EFDR calibration is too low.
Probability threshold automatically set equal to 'ProbThreshold'.
altExp 'spike-ins' is assumed to contain spike-in genes.
see help(altExp) for details. 

altExp 'spike-ins' is assumed to contain spike-in genes.
see help(altExp) for details. 

altExp 'spike-ins' is assumed to contain spike-in genes.
see help(altExp) for details. 

altExp 'spike-ins' is assumed to contain spike-in genes.
see help(altExp) for details. 

altExp 'spike-ins' is assumed to contain spike-in genes.
see help(altExp) for details. 

Running with spikes BASiCS sampler (regression case) ... 

-------------------------------------------------------------
MCMC running time 
-------------------------------------------------------------
user: 0.007
system: 0
elapsed: 0.006

-------------------------------------------------------------
Output 
-------------------------------------------------------------

-------------------------------------------------------------
BASiCS version 2.17.0 : 
vertical integration (spikes case) 
-------------------------------------------------------------

altExp 'spike-ins' is assumed to contain spike-in genes.
see help(altExp) for details. 

Running with spikes BASiCS sampler (regression case) ... 

-------------------------------------------------------------
MCMC running time 
-------------------------------------------------------------
user: 0.008
system: 0
elapsed: 0.008

-------------------------------------------------------------
Output 
-------------------------------------------------------------

-------------------------------------------------------------
BASiCS version 2.17.0 : 
vertical integration (spikes case) 
-------------------------------------------------------------

altExp 'spike-ins' is assumed to contain spike-in genes.
see help(altExp) for details. 

Running with spikes BASiCS sampler (regression case) ... 

-------------------------------------------------------------
MCMC running time 
-------------------------------------------------------------
user: 0.011
system: 0
elapsed: 0.011

-------------------------------------------------------------
Output 
-------------------------------------------------------------

-------------------------------------------------------------
BASiCS version 2.17.0 : 
vertical integration (spikes case) 
-------------------------------------------------------------

altExp 'spike-ins' is assumed to contain spike-in genes.
see help(altExp) for details. 

-------------------------------------------------------------
NOTE: default choice PriorDelta = 'log-normal'  (recommended value). 
Vallejos et al (2015) used a 'gamma' prior instead.
-------------------------------------------------------------

Running with spikes BASiCS sampler (no regression) ... 

-------------------------------------------------------------
MCMC running time 
-------------------------------------------------------------
user: 0.007
system: 0
elapsed: 0.006

-------------------------------------------------------------
Output 
-------------------------------------------------------------

-------------------------------------------------------------
BASiCS version 2.17.0 : 
vertical integration (spikes case) 
-------------------------------------------------------------

altExp 'spike-ins' is assumed to contain spike-in genes.
see help(altExp) for details. 

-------------------------------------------------------------
NOTE: default choice PriorDelta = 'log-normal'  (recommended value). 
Vallejos et al (2015) used a 'gamma' prior instead.
-------------------------------------------------------------

Running with spikes BASiCS sampler (no regression) ... 

-------------------------------------------------------------
MCMC running time 
-------------------------------------------------------------
user: 0.006
system: 0
elapsed: 0.007

-------------------------------------------------------------
Output 
-------------------------------------------------------------

-------------------------------------------------------------
BASiCS version 2.17.0 : 
vertical integration (spikes case) 
-------------------------------------------------------------

altExp 'spike-ins' is assumed to contain spike-in genes.
see help(altExp) for details. 

-------------------------------------------------------------
NOTE: default choice PriorDelta = 'log-normal'  (recommended value). 
Vallejos et al (2015) used a 'gamma' prior instead.
-------------------------------------------------------------

Running no spikes BASiCS sampler (no regression) ... 

-------------------------------------------------------------
MCMC running time 
-------------------------------------------------------------
user: 0.008
system: 0
elapsed: 0.008

-------------------------------------------------------------
Output 
-------------------------------------------------------------

-------------------------------------------------------------
NOTE: default choice PriorDelta = 'log-normal'  (recommended value). 
Vallejos et al (2015) used a 'gamma' prior instead.
-------------------------------------------------------------

Running no spikes BASiCS sampler (no regression) ... 

-------------------------------------------------------------
MCMC running time 
-------------------------------------------------------------
user: 0.01
system: 0
elapsed: 0.009

-------------------------------------------------------------
Output 
-------------------------------------------------------------

-------------------------------------------------------------
NOTE: default choice PriorDelta = 'log-normal'  (recommended value). 
Vallejos et al (2015) used a 'gamma' prior instead.
-------------------------------------------------------------

Running no spikes BASiCS sampler (no regression) ... 

-------------------------------------------------------------
MCMC running time 
-------------------------------------------------------------
user: 0.004
system: 0
elapsed: 0.004

-------------------------------------------------------------
Output 
-------------------------------------------------------------

-------------------------------------------------------------
NOTE: default choice PriorDelta = 'log-normal'  (recommended value). 
Vallejos et al (2015) used a 'gamma' prior instead.
-------------------------------------------------------------

Running no spikes BASiCS sampler (no regression) ... 

-------------------------------------------------------------
MCMC running time 
-------------------------------------------------------------
user: 0.004
system: 0
elapsed: 0.004

-------------------------------------------------------------
Output 
-------------------------------------------------------------

-------------------------------------------------------------
NOTE: default choice PriorDelta = 'log-normal'  (recommended value). 
Vallejos et al (2015) used a 'gamma' prior instead.
-------------------------------------------------------------

Running no spikes BASiCS sampler (no regression) ... 

-------------------------------------------------------------
MCMC running time 
-------------------------------------------------------------
user: 0.004
system: 0
elapsed: 0.004

-------------------------------------------------------------
Output 
-------------------------------------------------------------

altExp 'spike-ins' is assumed to contain spike-in genes.
see help(altExp) for details. 

altExp 'spike-ins' is assumed to contain spike-in genes.
see help(altExp) for details. 

Running no spikes BASiCS sampler (regression case) ... 

-------------------------------------------------------------
MCMC running time 
-------------------------------------------------------------
user: 0.008
system: 0
elapsed: 0.008

-------------------------------------------------------------
Output 
-------------------------------------------------------------

Running no spikes BASiCS sampler (regression case) ... 

-------------------------------------------------------------
MCMC running time 
-------------------------------------------------------------
user: 0.005
system: 0
elapsed: 0.005

-------------------------------------------------------------
Output 
-------------------------------------------------------------

Running no spikes BASiCS sampler (regression case) ... 

-------------------------------------------------------------
MCMC running time 
-------------------------------------------------------------
user: 0.006
system: 0
elapsed: 0.006

-------------------------------------------------------------
Output 
-------------------------------------------------------------

Running no spikes BASiCS sampler (regression case) ... 

-------------------------------------------------------------
MCMC running time 
-------------------------------------------------------------
user: 0.005
system: 0
elapsed: 0.006

-------------------------------------------------------------
Output 
-------------------------------------------------------------

Running no spikes BASiCS sampler (regression case) ... 

-------------------------------------------------------------
MCMC running time 
-------------------------------------------------------------
user: 0.006
system: 0
elapsed: 0.006

-------------------------------------------------------------
Output 
-------------------------------------------------------------

Running no spikes BASiCS sampler (regression case) ... 

-------------------------------------------------------------
MCMC running time 
-------------------------------------------------------------
user: 0.006
system: 0
elapsed: 0.006

-------------------------------------------------------------
Output 
-------------------------------------------------------------

-------------------------------------------------------------
NOTE: default choice PriorDelta = 'log-normal'  (recommended value). 
Vallejos et al (2015) used a 'gamma' prior instead.
-------------------------------------------------------------

Running no spikes BASiCS sampler (no regression) ... 

-------------------------------------------------------------
MCMC running time 
-------------------------------------------------------------
user: 0.01
system: 0
elapsed: 0.01

-------------------------------------------------------------
Output 
-------------------------------------------------------------

-------------------------------------------------------------
NOTE: default choice PriorDelta = 'log-normal'  (recommended value). 
Vallejos et al (2015) used a 'gamma' prior instead.
-------------------------------------------------------------

Running no spikes BASiCS sampler (no regression) ... 

-------------------------------------------------------------
MCMC running time 
-------------------------------------------------------------
user: 0.007
system: 0
elapsed: 0.008

-------------------------------------------------------------
Output 
-------------------------------------------------------------

-------------------------------------------------------------
NOTE: default choice PriorDelta = 'log-normal'  (recommended value). 
Vallejos et al (2015) used a 'gamma' prior instead.
-------------------------------------------------------------

Running no spikes BASiCS sampler (no regression) ... 

-------------------------------------------------------------
MCMC running time 
-------------------------------------------------------------
user: 0.008
system: 0
elapsed: 0.008

-------------------------------------------------------------
Output 
-------------------------------------------------------------

altExp 'spike-ins' is assumed to contain spike-in genes.
see help(altExp) for details. 

altExp 'spike-ins' is assumed to contain spike-in genes.
see help(altExp) for details. 

altExp 'spike-ins' is assumed to contain spike-in genes.
see help(altExp) for details. 

-------------------------------------------------------------
NOTE: default choice PriorDelta = 'log-normal'  (recommended value). 
Vallejos et al (2015) used a 'gamma' prior instead.
-------------------------------------------------------------

Running with spikes BASiCS sampler (no regression) ... 

-------------------------------------------------------------
MCMC running time 
-------------------------------------------------------------
user: 0.005
system: 0
elapsed: 0.005

-------------------------------------------------------------
Output 
-------------------------------------------------------------

-------------------------------------------------------------
BASiCS version 2.17.0 : 
vertical integration (spikes case) 
-------------------------------------------------------------

altExp 'spike-ins' is assumed to contain spike-in genes.
see help(altExp) for details. 

Running with spikes BASiCS sampler (regression case) ... 

-------------------------------------------------------------
MCMC running time 
-------------------------------------------------------------
user: 0.008
system: 0
elapsed: 0.008

-------------------------------------------------------------
Output 
-------------------------------------------------------------

-------------------------------------------------------------
BASiCS version 2.17.0 : 
vertical integration (spikes case) 
-------------------------------------------------------------

altExp 'spike-ins' is assumed to contain spike-in genes.
see help(altExp) for details. 

Running with spikes BASiCS sampler (regression case) ... 

-------------------------------------------------------------
MCMC running time 
-------------------------------------------------------------
user: 0.006
system: 0
elapsed: 0.006

-------------------------------------------------------------
Output 
-------------------------------------------------------------

-------------------------------------------------------------
BASiCS version 2.17.0 : 
vertical integration (spikes case) 
-------------------------------------------------------------

altExp 'spike-ins' is assumed to contain spike-in genes.
see help(altExp) for details. 

altExp 'spike-ins' is assumed to contain spike-in genes.
see help(altExp) for details. 

-------------------------------------------------------------
NOTE: default choice PriorDelta = 'log-normal'  (recommended value). 
Vallejos et al (2015) used a 'gamma' prior instead.
-------------------------------------------------------------

Running with spikes BASiCS sampler (no regression) ... 

-------------------------------------------------------------
MCMC running time 
-------------------------------------------------------------
user: 0.01
system: 0
elapsed: 0.01

-------------------------------------------------------------
Output 
-------------------------------------------------------------

-------------------------------------------------------------
BASiCS_Chain object stored as chain_.Rds file in
'/home/biocbuild/bbs-3.20-bioc/meat/BASiCS.Rcheck/tests/testthat' directory ... 
-------------------------------------------------------------

-------------------------------------------------------------
Storing trajectories of adaptive proposal variances (log-scale) aschain_ls_.Rds file in 
'/home/biocbuild/bbs-3.20-bioc/meat/BASiCS.Rcheck/tests/testthat' directory ... 
-------------------------------------------------------------

-------------------------------------------------------------
BASiCS version 2.17.0 : 
vertical integration (spikes case) 
-------------------------------------------------------------

altExp 'spike-ins' is assumed to contain spike-in genes.
see help(altExp) for details. 

Running with spikes BASiCS sampler (regression case) ... 

-------------------------------------------------------------
MCMC running time 
-------------------------------------------------------------
user: 0.01
system: 0
elapsed: 0.011

-------------------------------------------------------------
Output 
-------------------------------------------------------------

-------------------------------------------------------------
BASiCS_Chain object stored as chain_.Rds file in
'/home/biocbuild/bbs-3.20-bioc/meat/BASiCS.Rcheck/tests/testthat' directory ... 
-------------------------------------------------------------

-------------------------------------------------------------
Storing trajectories of adaptive proposal variances (log-scale) aschain_ls_.Rds file in 
'/home/biocbuild/bbs-3.20-bioc/meat/BASiCS.Rcheck/tests/testthat' directory ... 
-------------------------------------------------------------

-------------------------------------------------------------
BASiCS version 2.17.0 : 
vertical integration (spikes case) 
-------------------------------------------------------------

-------------------------------------------------------------
NOTE: default choice PriorDelta = 'log-normal'  (recommended value). 
Vallejos et al (2015) used a 'gamma' prior instead.
-------------------------------------------------------------

Running no spikes BASiCS sampler (no regression) ... 

-------------------------------------------------------------
MCMC running time 
-------------------------------------------------------------
user: 0.009
system: 0
elapsed: 0.009

-------------------------------------------------------------
Output 
-------------------------------------------------------------

-------------------------------------------------------------
BASiCS_Chain object stored as chain_.Rds file in
'/home/biocbuild/bbs-3.20-bioc/meat/BASiCS.Rcheck/tests/testthat' directory ... 
-------------------------------------------------------------

-------------------------------------------------------------
Storing trajectories of adaptive proposal variances (log-scale) aschain_ls_.Rds file in 
'/home/biocbuild/bbs-3.20-bioc/meat/BASiCS.Rcheck/tests/testthat' directory ... 
-------------------------------------------------------------

-------------------------------------------------------------
BASiCS version 2.17.0 : horizontal integration (no-spikes case)
-------------------------------------------------------------

Randomly, 1 out of 10
genes was left as reference at each iteration 
List of reference genes and frequencies stored as a .txt file in
'/home/biocbuild/bbs-3.20-bioc/meat/BASiCS.Rcheck/tests/testthat' directory ... 
-------------------------------------------------------------

Running no spikes BASiCS sampler (regression case) ... 

-------------------------------------------------------------
MCMC running time 
-------------------------------------------------------------
user: 0.01
system: 0
elapsed: 0.01

-------------------------------------------------------------
Output 
-------------------------------------------------------------

-------------------------------------------------------------
BASiCS_Chain object stored as chain_.Rds file in
'/home/biocbuild/bbs-3.20-bioc/meat/BASiCS.Rcheck/tests/testthat' directory ... 
-------------------------------------------------------------

-------------------------------------------------------------
Storing trajectories of adaptive proposal variances (log-scale) aschain_ls_.Rds file in 
'/home/biocbuild/bbs-3.20-bioc/meat/BASiCS.Rcheck/tests/testthat' directory ... 
-------------------------------------------------------------

-------------------------------------------------------------
BASiCS version 2.17.0 : horizontal integration (no-spikes case)
-------------------------------------------------------------

Randomly, 1 out of 10
genes was left as reference at each iteration 
List of reference genes and frequencies stored as a .txt file in
'/home/biocbuild/bbs-3.20-bioc/meat/BASiCS.Rcheck/tests/testthat' directory ... 
-------------------------------------------------------------

altExp 'spike-ins' is assumed to contain spike-in genes.
see help(altExp) for details. 

-------------------------------------------------------------
NOTE: default choice PriorDelta = 'log-normal'  (recommended value). 
Vallejos et al (2015) used a 'gamma' prior instead.
-------------------------------------------------------------

Running with spikes BASiCS sampler (no regression) ... 

-------------------------------------------------------------
MCMC running time 
-------------------------------------------------------------
user: 0.011
system: 0
elapsed: 0.011

-------------------------------------------------------------
Output 
-------------------------------------------------------------

-------------------------------------------------------------
BASiCS version 2.17.0 : 
vertical integration (spikes case) 
-------------------------------------------------------------

`BASiCS_Chain` class definition was outdated. 
Object updated to be compatible with BASiCS version 2.17.0.
Set 'StoreUpdatedChain' = TRUE to save updated object.

altExp 'spike-ins' is assumed to contain spike-in genes.
see help(altExp) for details. 

-------------------------------------------------------------
NOTE: default choice PriorDelta = 'log-normal'  (recommended value). 
Vallejos et al (2015) used a 'gamma' prior instead.
-------------------------------------------------------------

Running with spikes BASiCS sampler (no regression) ... 

-------------------------------------------------------------
MCMC running time 
-------------------------------------------------------------
user: 0.009
system: 0
elapsed: 0.009

-------------------------------------------------------------
Output 
-------------------------------------------------------------

-------------------------------------------------------------
BASiCS version 2.17.0 : 
vertical integration (spikes case) 
-------------------------------------------------------------

`BASiCS_Chain` class definition was outdated. 
Object updated to be compatible with BASiCS version 2.17.0.
Set 'StoreUpdatedChain' = TRUE to save updated object.
(this overwrites original input file).

-------------------------------------------------------------
Log-fold change thresholds are now set in a log2 scale. 
Original BASiCS release used a natural logarithm scale.
-------------------------------------------------------------
Offset estimate: 1
(ratio Group1 vs Group2).
-------------------------------------------------------------

EFDR calibration failed for Differential mean task. 
Probability threshold automatically set equal to 'ProbThresholdM'.
EFDR calibration failed for Differential dispersion task. 
Probability threshold automatically set equal to 'ProbThresholdD'.
EFDR calibration failed for Differential residual dispersion task. 
Probability threshold automatically set equal to 'ProbThresholdR'.
Running no spikes BASiCS sampler (regression case) ... 

-------------------------------------------------------------
MCMC running time 
-------------------------------------------------------------
user: 0.026
system: 0
elapsed: 0.026

-------------------------------------------------------------
Output 
-------------------------------------------------------------

-------------------------------------------------------------
Log-fold change thresholds are now set in a log2 scale. 
Original BASiCS release used a natural logarithm scale.
-------------------------------------------------------------
Offset estimate: 1
(ratio Group1 vs Group2).
-------------------------------------------------------------

EFDR calibration failed for Differential mean task. 
Probability threshold automatically set equal to 'ProbThresholdM'.
EFDR calibration failed for Differential dispersion task. 
Probability threshold automatically set equal to 'ProbThresholdD'.
EFDR calibration failed for Differential residual dispersion task. 
Probability threshold automatically set equal to 'ProbThresholdR'.
altExp 'spike-ins' is assumed to contain spike-in genes.
see help(altExp) for details. 

-------------------------------------------------------------
NOTE: default choice PriorDelta = 'log-normal'  (recommended value). 
Vallejos et al (2015) used a 'gamma' prior instead.
-------------------------------------------------------------

Running with spikes BASiCS sampler (no regression) ... 

-------------------------------------------------------------
MCMC running time 
-------------------------------------------------------------
user: 0.385
system: 0.004
elapsed: 0.389

-------------------------------------------------------------
Output 
-------------------------------------------------------------

-------------------------------------------------------------
BASiCS version 2.17.0 : 
vertical integration (spikes case) 
-------------------------------------------------------------

altExp 'spike-ins' is assumed to contain spike-in genes.
see help(altExp) for details. 

-------------------------------------------------------------
NOTE: default choice PriorDelta = 'log-normal'  (recommended value). 
Vallejos et al (2015) used a 'gamma' prior instead.
-------------------------------------------------------------

Running with spikes BASiCS sampler (no regression) ... 

-------------------------------------------------------------
MCMC running time 
-------------------------------------------------------------
user: 0.005
system: 0
elapsed: 0.004

-------------------------------------------------------------
Output 
-------------------------------------------------------------

-------------------------------------------------------------
Storing trajectories of adaptive proposal variances (log-scale) aschain_ls_.Rds file in 
'/home/biocbuild/bbs-3.20-bioc/meat/BASiCS.Rcheck/tests/testthat' directory ... 
-------------------------------------------------------------

-------------------------------------------------------------
BASiCS version 2.17.0 : 
vertical integration (spikes case) 
-------------------------------------------------------------

altExp 'spike-ins' is assumed to contain spike-in genes.
see help(altExp) for details. 

-------------------------------------------------------------
NOTE: default choice PriorDelta = 'log-normal'  (recommended value). 
Vallejos et al (2015) used a 'gamma' prior instead.
-------------------------------------------------------------

Running with spikes BASiCS sampler (no regression) ... 

-------------------------------------------------------------
MCMC running time 
-------------------------------------------------------------
user: 0.387
system: 0.004
elapsed: 0.391

-------------------------------------------------------------
Output 
-------------------------------------------------------------

-------------------------------------------------------------
BASiCS version 2.17.0 : 
vertical integration (spikes case) 
-------------------------------------------------------------

-------------------------------------------------------------
NOTE: default choice PriorDelta = 'log-normal'  (recommended value). 
Vallejos et al (2015) used a 'gamma' prior instead.
-------------------------------------------------------------

Running no spikes BASiCS sampler (no regression) ... 

-------------------------------------------------------------
MCMC running time 
-------------------------------------------------------------
user: 0.343
system: 0
elapsed: 0.344

-------------------------------------------------------------
Output 
-------------------------------------------------------------

-------------------------------------------------------------
NOTE: default choice PriorDelta = 'log-normal'  (recommended value). 
Vallejos et al (2015) used a 'gamma' prior instead.
-------------------------------------------------------------

Running no spikes BASiCS sampler (no regression) ... 

-------------------------------------------------------------
MCMC running time 
-------------------------------------------------------------
user: 0.339
system: 0.004
elapsed: 0.344

-------------------------------------------------------------
Output 
-------------------------------------------------------------

-------------------------------------------------------------
NOTE: default choice PriorDelta = 'log-normal'  (recommended value). 
Vallejos et al (2015) used a 'gamma' prior instead.
-------------------------------------------------------------

Running no spikes BASiCS sampler (no regression) ... 

-------------------------------------------------------------
MCMC running time 
-------------------------------------------------------------
user: 0.004
system: 0
elapsed: 0.004

-------------------------------------------------------------
Output 
-------------------------------------------------------------

-------------------------------------------------------------
Storing trajectories of adaptive proposal variances (log-scale) aschain_ls_.Rds file in 
'/home/biocbuild/bbs-3.20-bioc/meat/BASiCS.Rcheck/tests/testthat' directory ... 
-------------------------------------------------------------

-------------------------------------------------------------
NOTE: default choice PriorDelta = 'log-normal'  (recommended value). 
Vallejos et al (2015) used a 'gamma' prior instead.
-------------------------------------------------------------

Running no spikes BASiCS sampler (no regression) ... 

-------------------------------------------------------------
MCMC running time 
-------------------------------------------------------------
user: 0.345
system: 0.004
elapsed: 0.349

-------------------------------------------------------------
Output 
-------------------------------------------------------------

-------------------------------------------------------------
NOTE: default choice PriorDelta = 'log-normal'  (recommended value). 
Vallejos et al (2015) used a 'gamma' prior instead.
-------------------------------------------------------------

Running no spikes BASiCS sampler (no regression) ... 

-------------------------------------------------------------
MCMC running time 
-------------------------------------------------------------
user: 0.349
system: 0
elapsed: 0.35

-------------------------------------------------------------
Output 
-------------------------------------------------------------

Running no spikes BASiCS sampler (regression case) ... 

-------------------------------------------------------------
MCMC running time 
-------------------------------------------------------------
user: 0.623
system: 0.004
elapsed: 0.629

-------------------------------------------------------------
Output 
-------------------------------------------------------------

Running no spikes BASiCS sampler (regression case) ... 

-------------------------------------------------------------
MCMC running time 
-------------------------------------------------------------
user: 0.622
system: 0
elapsed: 0.623

-------------------------------------------------------------
Output 
-------------------------------------------------------------

Running no spikes BASiCS sampler (regression case) ... 

-------------------------------------------------------------
MCMC running time 
-------------------------------------------------------------
user: 0.025
system: 0
elapsed: 0.025

-------------------------------------------------------------
Output 
-------------------------------------------------------------

-------------------------------------------------------------
Storing trajectories of adaptive proposal variances (log-scale) aschain_ls_.Rds file in 
'/home/biocbuild/bbs-3.20-bioc/meat/BASiCS.Rcheck/tests/testthat' directory ... 
-------------------------------------------------------------

altExp 'spike-ins' is assumed to contain spike-in genes.
see help(altExp) for details. 

Running with spikes BASiCS sampler (regression case) ... 

-------------------------------------------------------------
MCMC running time 
-------------------------------------------------------------
user: 0.487
system: 0
elapsed: 0.487

-------------------------------------------------------------
Output 
-------------------------------------------------------------

-------------------------------------------------------------
BASiCS version 2.17.0 : 
vertical integration (spikes case) 
-------------------------------------------------------------

altExp 'spike-ins' is assumed to contain spike-in genes.
see help(altExp) for details. 

Running with spikes BASiCS sampler (regression case) ... 

-------------------------------------------------------------
MCMC running time 
-------------------------------------------------------------
user: 0.007
system: 0
elapsed: 0.007

-------------------------------------------------------------
Output 
-------------------------------------------------------------

-------------------------------------------------------------
Storing trajectories of adaptive proposal variances (log-scale) aschain_ls_.Rds file in 
'/home/biocbuild/bbs-3.20-bioc/meat/BASiCS.Rcheck/tests/testthat' directory ... 
-------------------------------------------------------------

-------------------------------------------------------------
BASiCS version 2.17.0 : 
vertical integration (spikes case) 
-------------------------------------------------------------

-------------------------------------------------------------
Log-fold change thresholds are now set in a log2 scale. 
Original BASiCS release used a natural logarithm scale.
-------------------------------------------------------------
Offset estimate: 0.6714
(ratio Group1 vs Group2).
To visualise its effect, please use 'PlotOffset = TRUE'.
-------------------------------------------------------------

For Differential mean task:
the posterior probability threshold chosen via EFDR calibration is too low.
Probability threshold automatically set equal to 'ProbThresholdM'.
EFDR calibration failed for Differential dispersion task. 
Probability threshold automatically set equal to 'ProbThresholdD'.
-------------------------------------------------------------
Log-fold change thresholds are now set in a log2 scale. 
Original BASiCS release used a natural logarithm scale.
-------------------------------------------------------------
Offset estimate: 0.6787
(ratio Group1 vs Group2).
To visualise its effect, please use 'PlotOffset = TRUE'.
-------------------------------------------------------------

EFDR calibration failed for Differential mean task. 
Probability threshold automatically set equal to 'ProbThresholdM'.
EFDR calibration failed for Differential dispersion task. 
Probability threshold automatically set equal to 'ProbThresholdD'.
For Differential residual dispersion task:
the posterior probability threshold chosen via EFDR calibration is too low.
Probability threshold automatically set equal to 'ProbThresholdR'.
altExp 'spike-ins' is assumed to contain spike-in genes.
see help(altExp) for details. 

Running with spikes BASiCS sampler (regression case) ... 

-------------------------------------------------------------
MCMC running time 
-------------------------------------------------------------
user: 0.013
system: 0
elapsed: 0.013

-------------------------------------------------------------
Output 
-------------------------------------------------------------

-------------------------------------------------------------
BASiCS version 2.17.0 : 
vertical integration (spikes case) 
-------------------------------------------------------------

altExp 'spike-ins' is assumed to contain spike-in genes.
see help(altExp) for details. 

Running with spikes BASiCS sampler (regression case) ... 

-------------------------------------------------------------
MCMC running time 
-------------------------------------------------------------
user: 0.007
system: 0
elapsed: 0.007

-------------------------------------------------------------
Output 
-------------------------------------------------------------

-------------------------------------------------------------
BASiCS version 2.17.0 : 
vertical integration (spikes case) 
-------------------------------------------------------------

altExp 'spike-ins' is assumed to contain spike-in genes.
see help(altExp) for details. 

Running with spikes BASiCS sampler (regression case) ... 

-------------------------------------------------------------
MCMC running time 
-------------------------------------------------------------
user: 0.01
system: 0
elapsed: 0.01

-------------------------------------------------------------
Output 
-------------------------------------------------------------

-------------------------------------------------------------
BASiCS version 2.17.0 : 
vertical integration (spikes case) 
-------------------------------------------------------------

altExp 'spike-ins' is assumed to contain spike-in genes.
see help(altExp) for details. 

Running with spikes BASiCS sampler (regression case) ... 

-------------------------------------------------------------
MCMC running time 
-------------------------------------------------------------
user: 0.006
system: 0
elapsed: 0.006

-------------------------------------------------------------
Output 
-------------------------------------------------------------

-------------------------------------------------------------
BASiCS version 2.17.0 : 
vertical integration (spikes case) 
-------------------------------------------------------------

altExp 'spike-ins' is assumed to contain spike-in genes.
see help(altExp) for details. 

'BatchInfo' was treated as a factor with 2 levels: 
1  2  
'BatchInfo' was treated as a factor with 2 levels: 
1  2  
-------------------------------------------------------------
NOTE: default choice PriorDelta = 'log-normal'  (recommended value). 
Vallejos et al (2015) used a 'gamma' prior instead.
-------------------------------------------------------------

Running no spikes BASiCS sampler (no regression) ... 

-------------------------------------------------------------
MCMC running time 
-------------------------------------------------------------
user: 0.012
system: 0
elapsed: 0.013

-------------------------------------------------------------
Output 
-------------------------------------------------------------

'BatchInfo' was treated as a factor with 2 levels: 
1  2  
altExp 'spike-ins' is assumed to contain spike-in genes.
see help(altExp) for details. 

-------------------------------------------------------------
NOTE: default choice PriorDelta = 'log-normal'  (recommended value). 
Vallejos et al (2015) used a 'gamma' prior instead.
-------------------------------------------------------------

Running with spikes BASiCS sampler (no regression) ... 

-------------------------------------------------------------
MCMC running time 
-------------------------------------------------------------
user: 0.006
system: 0
elapsed: 0.006

-------------------------------------------------------------
Output 
-------------------------------------------------------------

-------------------------------------------------------------
BASiCS version 2.17.0 : 
vertical integration (spikes case) 
-------------------------------------------------------------

[ FAIL 0 | WARN 0 | SKIP 0 | PASS 459 ]
> 
> proc.time()
   user  system elapsed 
330.421   6.013 367.409

Example timings

BASiCS.Rcheck/BASiCS-Ex.timings

name	user	system	elapsed
BASiCS_Chain-methods	4.179	0.251	4.442
BASiCS_Chain	5.481	0.196	5.692
BASiCS_CorrectOffset	0.018	0.000	0.018
BASiCS_DenoisedCounts	3.382	0.131	3.522
BASiCS_DenoisedRates	3.317	0.093	3.422
BASiCS_DetectVG	1.109	0.051	1.164
BASiCS_DiagHist	1.445	0.028	1.476
BASiCS_DiagPlot	2.997	0.056	3.068
BASiCS_DivideAndConquer	4.084	0.161	22.538
BASiCS_Draw	0.578	0.020	0.599
BASiCS_EffectiveSize	0.321	0.012	0.334
BASiCS_Filter	0.002	0.000	0.002
BASiCS_LoadChain	2.991	0.176	3.173
BASiCS_MCMC	10.342	0.355	10.717
BASiCS_MockSCE	0.557	0.020	0.578
BASiCS_PlotDE	4.737	0.096	4.843
BASiCS_PlotOffset	1.361	0.016	1.380
BASiCS_PlotVG	0.515	0.004	0.519
BASiCS_PriorParam	0.416	0.008	0.424
BASiCS_ShowFit	0.325	0.016	0.342
BASiCS_Sim	1.284	0.032	1.318
BASiCS_Summary-methods	0.006	0.000	0.005
BASiCS_Summary	3.137	0.108	3.252
BASiCS_TestDE	9.543	0.147	9.708
BASiCS_VarThresholdSearchHVG_LVG	3.096	0.012	3.113
BASiCS_VarianceDecomp	0.254	0.004	0.259
Summary-BASiCS_Chain-method	0.287	0.012	0.299
dim-BASiCS_Chain-method	0.006	0.000	0.006
dimnames-BASiCS_Chain-method	0.001	0.005	0.006
displayChainBASiCS-BASiCS_Chain-method	0.154	0.026	0.200
displaySummaryBASiCS-BASiCS_Summary-method	0.152	0.011	0.164
makeExampleBASiCS_Data	0.468	0.004	0.473
newBASiCS_Chain	6.014	0.128	6.153
plot-BASiCS_Chain-method	0.143	0.018	0.161
plot-BASiCS_Summary-method	0.156	0.007	0.164
show-BASiCS_ResultDE-method	0.148	0.011	0.160
show-BASiCS_ResultVG-method	0.156	0.000	0.157
show-BASiCS_ResultsDE-method	0.142	0.015	0.158
subset-BASiCS_Chain-method	1.334	0.012	1.349