Back to Multiple platform build/check report for BioC 3.22:   simplified   long
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This page was generated on 2025-08-04 12:12 -0400 (Mon, 04 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.2 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4796
palomino8Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4536
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4578
kjohnson3macOS 13.7.1 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4519
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4517
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

Package 136/2313HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BASiCS 2.21.0  (landing page)
Catalina Vallejos
Snapshot Date: 2025-08-03 13:25 -0400 (Sun, 03 Aug 2025)
git_url: https://git.bioconductor.org/packages/BASiCS
git_branch: devel
git_last_commit: de11c8b
git_last_commit_date: 2025-04-15 11:14:38 -0400 (Tue, 15 Apr 2025)
nebbiolo2Linux (Ubuntu 24.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  NO, package depends on 'scran' which is only available as a source package that needs compilation
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for BASiCS on taishan

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: 2.21.0
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_2.21.0.tar.gz
StartedAt: 2025-08-01 04:19:14 -0000 (Fri, 01 Aug 2025)
EndedAt: 2025-08-01 04:30:11 -0000 (Fri, 01 Aug 2025)
EllapsedTime: 656.5 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_2.21.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/BASiCS.Rcheck’
* using R version 4.5.0 (2025-04-11)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BASiCS/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BASiCS’ version ‘2.21.0’
* 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: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’
* checking C++ specification ... NOTE
  Specified C++11: please drop specification unless essential
* checking installed package size ... INFO
  installed size is 11.5Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   8.5Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking 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 ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  BASiCS_DenoisedCounts.Rd: SingleCellExperiment-class
  BASiCS_DenoisedRates.Rd: SingleCellExperiment-class
  BASiCS_DivideAndConquer.Rd: BiocParallelParam
  BASiCS_Draw.Rd: SingleCellExperiment-class
  BASiCS_Filter.Rd: SingleCellExperiment-class
  BASiCS_MCMC.Rd: SingleCellExperiment-class, BiocParallelParam
  BASiCS_MockSCE.Rd: SingleCellExperiment-class
  BASiCS_PriorParam.Rd: SingleCellExperiment-class
  BASiCS_ResultVG.Rd: DataFrame-class
  BASiCS_Sim.Rd: SingleCellExperiment-class
  BASiCS_VarianceDecomp.Rd: scale_fill_brewer
  makeExampleBASiCS_Data.Rd: SingleCellExperiment-class
  newBASiCS_Data.Rd: SingleCellExperiment-class
  rowData.Rd: DFrame-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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_TestDE           9.619  0.056   9.701
BASiCS_MCMC             8.191  0.092   8.308
BASiCS_DivideAndConquer 3.032  0.118  20.083
* 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-3.22-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-4.5.0/site-library’
* installing *source* package ‘BASiCS’ ...
** this is package ‘BASiCS’ version ‘2.21.0’
** using staged installation
** libs
using C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’
using C++11
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0/site-library/RcppArmadillo/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -Werror=format-security  -c BASiCS.cpp -o BASiCS.o
In file included from /home/biocbuild/R/R-4.5.0/include/R.h:73,
                 from libraries.h:6,
                 from utils.h:4,
                 from updates.h:4,
                 from BASiCS.cpp:1:
/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include/Rcpp/exceptions.h: In function ‘void Rcpp::Rf_warning(const char*, Args&& ...) [with Args = {const char*}]’:
/home/biocbuild/R/R-4.5.0/include/R_ext/Error.h:85:17: warning: infinite recursion detected [-Winfinite-recursion]
   85 | #define warning Rf_warning
      |                 ^~~~~~~~~~
/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include/Rcpp/exceptions.h:190:17: note: in expansion of macro ‘warning’
  190 |     inline void warning(const char* fmt, Args&&... args ) {
      |                 ^~~~~~~
In file included from /home/biocbuild/R/R-4.5.0/site-library/Rcpp/include/RcppCommon.h:133,
                 from /home/biocbuild/R/R-4.5.0/site-library/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:25,
                 from /home/biocbuild/R/R-4.5.0/site-library/RcppArmadillo/include/RcppArmadillo.h:29,
                 from libraries.h:11:
/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include/Rcpp/exceptions.h:191:19: note: recursive call
  191 |         Rf_warning("%s", tfm::format(fmt, std::forward<Args>(args)... ).c_str());
      |         ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0/site-library/RcppArmadillo/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -Werror=format-security  -c RcppExports.cpp -o RcppExports.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -shared -L/home/biocbuild/R/R-4.5.0/lib -L/usr/local/lib -o BASiCS.so BASiCS.o RcppExports.o -lopenblas -lgfortran -lm -fopenmp -L/home/biocbuild/R/R-4.5.0/lib -lR
installing to /home/biocbuild/R/R-4.5.0/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 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
Copyright (C) 2025 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
Loading required package: generics

Attaching package: 'generics'

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

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


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, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, 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: Seqinfo
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: 0.011
system: 0
elapsed: 0.011

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

-------------------------------------------------------------
BASiCS version 2.21.0 : 
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: 0.013
system: 0
elapsed: 0.013

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

-------------------------------------------------------------
BASiCS version 2.21.0 : 
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: 0.01
system: 0
elapsed: 0.011

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

-------------------------------------------------------------
BASiCS version 2.21.0 : 
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: 0.014
system: 0
elapsed: 0.014

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

-------------------------------------------------------------
BASiCS version 2.21.0 : 
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: 0.006
system: 0.004
elapsed: 0.012

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

-------------------------------------------------------------
BASiCS version 2.21.0 : 
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: 0.013
system: 0
elapsed: 0.013

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

-------------------------------------------------------------
BASiCS version 2.21.0 : 
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: 0.01
system: 0
elapsed: 0.011

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

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

-------------------------------------------------------------
MCMC running time 
-------------------------------------------------------------
user: 0.012
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: 0.008
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: 0.011
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
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: 0.012
system: 0
elapsed: 0.013

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

-------------------------------------------------------------
BASiCS version 2.21.0 : 
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: 0.013
system: 0
elapsed: 0.013

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

-------------------------------------------------------------
BASiCS version 2.21.0 : 
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: 0.01
system: 0
elapsed: 0.01

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

-------------------------------------------------------------
BASiCS version 2.21.0 : 
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: 0.013
system: 0
elapsed: 0.013

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

-------------------------------------------------------------
BASiCS version 2.21.0 : 
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: 0.011
system: 0
elapsed: 0.011

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

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

-------------------------------------------------------------
MCMC running time 
-------------------------------------------------------------
user: 0.011
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: 0.007
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: 0.011
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
-------------------------------------------------------------
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: 0.016

-------------------------------------------------------------
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: 0.063
system: 0
elapsed: 0.064

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

-------------------------------------------------------------
BASiCS version 2.21.0 : 
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: 0.066
system: 0
elapsed: 0.067

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

-------------------------------------------------------------
BASiCS version 2.21.0 : 
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: 0.07

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

-------------------------------------------------------------
BASiCS version 2.21.0 : 
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: 0.058
system: 0
elapsed: 0.059

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

-------------------------------------------------------------
BASiCS version 2.21.0 : 
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: 17
RefGene: 11
RefGene: 11
RefGene: 0
RefGene: 43
RefGene: 16
RefGene: 15
RefGene: 44
RefGene: 17
RefGene: 17
RefGene: 11
RefGene: 0
RefGene: 39
RefGene: 16
RefGene: 43
RefGene: 39
RefGene: 13
RefGene: 0
RefGene: 17
RefGene: 13
RefGene: 44
RefGene: 0
RefGene: 39
RefGene: 31
RefGene: 13
RefGene: 44
RefGene: 15
RefGene: 39
RefGene: 11
RefGene: 13
RefGene: 0
RefGene: 13
RefGene: 16
RefGene: 17
RefGene: 15
RefGene: 11
RefGene: 17
RefGene: 39
RefGene: 16
RefGene: 15
RefGene: 17
RefGene: 13
RefGene: 15
RefGene: 15
RefGene: 13
RefGene: 17
RefGene: 13
RefGene: 15
RefGene: 31
RefGene: 0
RefGene: 43
RefGene: 31
RefGene: 43
RefGene: 0
RefGene: 0
RefGene: 17
RefGene: 44
RefGene: 13
RefGene: 31
RefGene: 11
RefGene: 44
RefGene: 17
RefGene: 43
RefGene: 39
RefGene: 39
RefGene: 44
RefGene: 13
RefGene: 16
RefGene: 43
RefGene: 11
RefGene: 15
RefGene: 11
RefGene: 16
RefGene: 43
RefGene: 44
RefGene: 13
RefGene: 15
RefGene: 11
RefGene: 11
RefGene: 44
RefGene: 16
RefGene: 16
RefGene: 44
RefGene: 44
RefGene: 31
RefGene: 43
RefGene: 44
RefGene: 11
RefGene: 11
RefGene: 11
RefGene: 44
RefGene: 43
RefGene: 11
RefGene: 44
RefGene: 13
RefGene: 17
RefGene: 0
RefGene: 11
RefGene: 31
RefGene: 17
-----------------------------------------------------
End of Burn-in period.
-----------------------------------------------------
RefGene: 44
RefGene: 31
RefGene: 31
RefGene: 0
RefGene: 11
RefGene: 44
RefGene: 17
RefGene: 17
RefGene: 44
RefGene: 31
RefGene: 44
RefGene: 13
RefGene: 43
RefGene: 0
RefGene: 13
RefGene: 11
RefGene: 15
RefGene: 15
RefGene: 13
RefGene: 16
RefGene: 15
RefGene: 39
RefGene: 11
RefGene: 43
RefGene: 39
RefGene: 11
RefGene: 39
RefGene: 0
RefGene: 43
RefGene: 43
RefGene: 13
RefGene: 16
RefGene: 15
RefGene: 15
RefGene: 0
RefGene: 31
RefGene: 39
RefGene: 16
RefGene: 31
RefGene: 11
RefGene: 44
RefGene: 16
RefGene: 16
RefGene: 39
RefGene: 17
RefGene: 17
RefGene: 31
RefGene: 13
RefGene: 17
RefGene: 31
RefGene: 17
RefGene: 43
RefGene: 0
RefGene: 15
RefGene: 39
RefGene: 17
RefGene: 0
RefGene: 43
RefGene: 31
RefGene: 31
RefGene: 44
RefGene: 17
RefGene: 15
RefGene: 39
RefGene: 44
RefGene: 39
RefGene: 13
RefGene: 31
RefGene: 43
RefGene: 39
RefGene: 15
RefGene: 39
RefGene: 39
RefGene: 17
RefGene: 44
RefGene: 11
RefGene: 0
RefGene: 0
RefGene: 31
RefGene: 0
RefGene: 0
RefGene: 15
RefGene: 31
RefGene: 13
RefGene: 0
RefGene: 16
RefGene: 15
RefGene: 39
RefGene: 16
RefGene: 13
RefGene: 0
RefGene: 31
RefGene: 31
RefGene: 31
RefGene: 16
RefGene: 0
RefGene: 43
RefGene: 11
RefGene: 13
RefGene: 13
 
-----------------------------------------------------
-----------------------------------------------------
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: 0.4918
Maximum acceptance rate among mu[i]'s: 0.78
 
 
Minimum acceptance rate among delta[i]'s: 0.57
Average acceptance rate among delta[i]'s: 0.6732
Maximum acceptance rate among delta[i]'s: 0.86
 
 
Minimum acceptance rate among nu[jk]'s: 0.79
Average acceptance rate among nu[jk]'s: 0.9513
Maximum acceptance rate among nu[jk]'s: 1
 
 
Minimum acceptance rate among theta[k]'s: 1
Average acceptance rate among theta[k]'s: 1
Maximum acceptance rate among theta[k]'s: 1
 
-----------------------------------------------------
 
-------------------------------------------------------------
MCMC running time 
-------------------------------------------------------------
user: 0.198
system: 0
elapsed: 0.198

-------------------------------------------------------------
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: 47
RefGene: 19
RefGene: 23
RefGene: 49
RefGene: 9
RefGene: 9
RefGene: 19
RefGene: 14
RefGene: 9
RefGene: 10
RefGene: 23
RefGene: 19
RefGene: 10
RefGene: 9
RefGene: 19
RefGene: 22
RefGene: 47
RefGene: 11
RefGene: 9
RefGene: 22
RefGene: 22
RefGene: 22
RefGene: 10
RefGene: 19
RefGene: 49
RefGene: 36
RefGene: 23
RefGene: 47
RefGene: 36
RefGene: 9
RefGene: 23
RefGene: 22
RefGene: 10
RefGene: 22
RefGene: 11
RefGene: 14
RefGene: 23
RefGene: 36
RefGene: 49
RefGene: 22
RefGene: 36
RefGene: 49
RefGene: 22
RefGene: 22
RefGene: 23
RefGene: 10
RefGene: 9
RefGene: 10
RefGene: 9
RefGene: 14
RefGene: 47
RefGene: 9
RefGene: 10
RefGene: 36
RefGene: 49
RefGene: 47
RefGene: 49
RefGene: 22
RefGene: 9
RefGene: 14
RefGene: 23
RefGene: 47
RefGene: 11
RefGene: 14
RefGene: 49
RefGene: 23
RefGene: 9
RefGene: 9
RefGene: 19
RefGene: 47
RefGene: 23
RefGene: 36
RefGene: 10
RefGene: 14
RefGene: 14
RefGene: 23
RefGene: 19
RefGene: 22
RefGene: 36
RefGene: 22
RefGene: 14
RefGene: 36
RefGene: 36
RefGene: 36
RefGene: 49
RefGene: 19
RefGene: 19
RefGene: 22
RefGene: 11
RefGene: 19
RefGene: 10
RefGene: 47
RefGene: 11
RefGene: 49
RefGene: 19
RefGene: 19
RefGene: 23
RefGene: 11
RefGene: 9
-----------------------------------------------------
End of Burn-in period.
-----------------------------------------------------
RefGene: 9
RefGene: 49
RefGene: 10
RefGene: 47
RefGene: 10
RefGene: 36
RefGene: 10
RefGene: 19
RefGene: 10
RefGene: 14
RefGene: 47
RefGene: 23
RefGene: 36
RefGene: 11
RefGene: 10
RefGene: 14
RefGene: 23
RefGene: 36
RefGene: 9
RefGene: 22
RefGene: 22
RefGene: 11
RefGene: 11
RefGene: 19
RefGene: 47
RefGene: 10
RefGene: 23
RefGene: 47
RefGene: 11
RefGene: 36
RefGene: 10
RefGene: 22
RefGene: 9
RefGene: 47
RefGene: 47
RefGene: 22
RefGene: 14
RefGene: 47
RefGene: 9
RefGene: 22
RefGene: 14
RefGene: 10
RefGene: 22
RefGene: 19
RefGene: 14
RefGene: 49
RefGene: 22
RefGene: 10
RefGene: 9
RefGene: 14
RefGene: 47
RefGene: 49
RefGene: 9
RefGene: 23
RefGene: 49
RefGene: 9
RefGene: 10
RefGene: 23
RefGene: 9
RefGene: 49
RefGene: 23
RefGene: 14
RefGene: 14
RefGene: 19
RefGene: 19
RefGene: 11
RefGene: 9
RefGene: 47
RefGene: 9
RefGene: 11
RefGene: 10
RefGene: 10
RefGene: 23
RefGene: 11
RefGene: 23
RefGene: 47
RefGene: 36
RefGene: 19
RefGene: 14
RefGene: 22
RefGene: 23
RefGene: 14
RefGene: 14
RefGene: 10
RefGene: 23
RefGene: 22
RefGene: 36
RefGene: 11
RefGene: 14
RefGene: 22
RefGene: 23
RefGene: 36
RefGene: 19
RefGene: 22
RefGene: 49
RefGene: 49
RefGene: 10
RefGene: 10
RefGene: 47
RefGene: 19
 
-----------------------------------------------------
-----------------------------------------------------
All 200 MCMC iterations have been completed.
-----------------------------------------------------
-----------------------------------------------------
 
-----------------------------------------------------
Please see below a summary of the overall acceptance rates.
-----------------------------------------------------
 
Minimum acceptance rate among mu[i]'s: 0.23
Average acceptance rate among mu[i]'s: 0.5146
Maximum acceptance rate among mu[i]'s: 0.76
 
 
Minimum acceptance rate among delta[i]'s: 0.51
Average acceptance rate among delta[i]'s: 0.6608
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: 0.9587
Maximum acceptance rate among nu[jk]'s: 1
 
 
Minimum acceptance rate among theta[k]'s: 0
Average acceptance rate among theta[k]'s: 0
Maximum acceptance rate among theta[k]'s: 0
 
-----------------------------------------------------
 
-------------------------------------------------------------
MCMC running time 
-------------------------------------------------------------
user: 0.199
system: 0
elapsed: 0.199

-------------------------------------------------------------
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: 0.006
system: 0
elapsed: 0.007

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

-------------------------------------------------------------
BASiCS version 2.21.0 : 
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: 0.009
system: 0
elapsed: 0.009

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

-------------------------------------------------------------
BASiCS version 2.21.0 : 
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 2.21.0 : 
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 2.21.0 : 
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: 0.005

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

-------------------------------------------------------------
BASiCS version 2.21.0 : 
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: 0.01
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: 0.007
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: 0.004
system: 0
elapsed: 0.005

-------------------------------------------------------------
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: 0.006
system: 0
elapsed: 0.006

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

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: 0.006

-------------------------------------------------------------
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: 0.005

-------------------------------------------------------------
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 
-------------------------------------------------------------

-------------------------------------------------------------
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: 0.008
system: 0
elapsed: 0.007

-------------------------------------------------------------
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: 0.007
system: 0
elapsed: 0.008

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

-------------------------------------------------------------
BASiCS version 2.21.0 : 
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 2.21.0 : 
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: 0.008

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

-------------------------------------------------------------
BASiCS version 2.21.0 : 
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: 0.009
system: 0
elapsed: 0.009

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

-------------------------------------------------------------
BASiCS_Chain object stored as chain_.Rds file in
'/home/biocbuild/bbs-3.22-bioc/meat/BASiCS.Rcheck/tests/testthat' directory ... 
-------------------------------------------------------------

-------------------------------------------------------------
Storing trajectories of adaptive proposal variances (log-scale) aschain_ls_.Rds file in 
'/home/biocbuild/bbs-3.22-bioc/meat/BASiCS.Rcheck/tests/testthat' directory ... 
-------------------------------------------------------------

-------------------------------------------------------------
BASiCS version 2.21.0 : 
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: 0.013
system: 0
elapsed: 0.013

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

-------------------------------------------------------------
BASiCS_Chain object stored as chain_.Rds file in
'/home/biocbuild/bbs-3.22-bioc/meat/BASiCS.Rcheck/tests/testthat' directory ... 
-------------------------------------------------------------

-------------------------------------------------------------
Storing trajectories of adaptive proposal variances (log-scale) aschain_ls_.Rds file in 
'/home/biocbuild/bbs-3.22-bioc/meat/BASiCS.Rcheck/tests/testthat' directory ... 
-------------------------------------------------------------

-------------------------------------------------------------
BASiCS version 2.21.0 : 
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: 0.007
system: 0
elapsed: 0.007

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

-------------------------------------------------------------
BASiCS_Chain object stored as chain_.Rds file in
'/home/biocbuild/bbs-3.22-bioc/meat/BASiCS.Rcheck/tests/testthat' directory ... 
-------------------------------------------------------------

-------------------------------------------------------------
Storing trajectories of adaptive proposal variances (log-scale) aschain_ls_.Rds file in 
'/home/biocbuild/bbs-3.22-bioc/meat/BASiCS.Rcheck/tests/testthat' directory ... 
-------------------------------------------------------------

-------------------------------------------------------------
BASiCS version 2.21.0 : 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-3.22-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-3.22-bioc/meat/BASiCS.Rcheck/tests/testthat' directory ... 
-------------------------------------------------------------

-------------------------------------------------------------
Storing trajectories of adaptive proposal variances (log-scale) aschain_ls_.Rds file in 
'/home/biocbuild/bbs-3.22-bioc/meat/BASiCS.Rcheck/tests/testthat' directory ... 
-------------------------------------------------------------

-------------------------------------------------------------
BASiCS version 2.21.0 : 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-3.22-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: 0.009
system: 0.001
elapsed: 0.009

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

-------------------------------------------------------------
BASiCS version 2.21.0 : 
vertical integration (spikes case) 
-------------------------------------------------------------

`BASiCS_Chain` class definition was outdated. 
Object updated to be compatible with BASiCS version 2.21.0.
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: 0.011
system: 0
elapsed: 0.01

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

-------------------------------------------------------------
BASiCS version 2.21.0 : 
vertical integration (spikes case) 
-------------------------------------------------------------

`BASiCS_Chain` class definition was outdated. 
Object updated to be compatible with BASiCS version 2.21.0.
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: 0.027

-------------------------------------------------------------
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: 0.378
system: 0
elapsed: 0.379

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

-------------------------------------------------------------
BASiCS version 2.21.0 : 
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: 0.005

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

-------------------------------------------------------------
Storing trajectories of adaptive proposal variances (log-scale) aschain_ls_.Rds file in 
'/home/biocbuild/bbs-3.22-bioc/meat/BASiCS.Rcheck/tests/testthat' directory ... 
-------------------------------------------------------------

-------------------------------------------------------------
BASiCS version 2.21.0 : 
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: 0.381
system: 0
elapsed: 0.382

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

-------------------------------------------------------------
BASiCS version 2.21.0 : 
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: 0.323
system: 0.008
elapsed: 0.332

-------------------------------------------------------------
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: 0.331
system: 0
elapsed: 0.332

-------------------------------------------------------------
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: 0.005

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

-------------------------------------------------------------
Storing trajectories of adaptive proposal variances (log-scale) aschain_ls_.Rds file in 
'/home/biocbuild/bbs-3.22-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: 0.332
system: 0.004
elapsed: 0.338

-------------------------------------------------------------
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: 0.333
system: 0.004
elapsed: 0.338

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

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

-------------------------------------------------------------
MCMC running time 
-------------------------------------------------------------
user: 0.575
system: 0.012
elapsed: 0.59

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

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

-------------------------------------------------------------
MCMC running time 
-------------------------------------------------------------
user: 0.577
system: 0.012
elapsed: 0.591

-------------------------------------------------------------
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-3.22-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: 0.476
system: 0.004
elapsed: 0.482

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

-------------------------------------------------------------
BASiCS version 2.21.0 : 
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 
-------------------------------------------------------------

-------------------------------------------------------------
Storing trajectories of adaptive proposal variances (log-scale) aschain_ls_.Rds file in 
'/home/biocbuild/bbs-3.22-bioc/meat/BASiCS.Rcheck/tests/testthat' directory ... 
-------------------------------------------------------------

-------------------------------------------------------------
BASiCS version 2.21.0 : 
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: 0.011
system: 0
elapsed: 0.011

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

-------------------------------------------------------------
BASiCS version 2.21.0 : 
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 2.21.0 : 
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 2.21.0 : 
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 2.21.0 : 
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: 0.009
system: 0
elapsed: 0.009

-------------------------------------------------------------
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: 0.002
system: 0.004
elapsed: 0.005

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

-------------------------------------------------------------
BASiCS version 2.21.0 : 
vertical integration (spikes case) 
-------------------------------------------------------------

[ FAIL 0 | WARN 0 | SKIP 0 | PASS 459 ]
> 
> proc.time()
   user  system elapsed 
248.125   4.841 282.501 

Example timings

BASiCS.Rcheck/BASiCS-Ex.timings

nameusersystemelapsed
BASiCS_Chain-methods2.9370.4143.361
BASiCS_Chain3.6090.0923.710
BASiCS_CorrectOffset0.0140.0040.019
BASiCS_DenoisedCounts2.3280.0282.362
BASiCS_DenoisedRates2.1540.0442.202
BASiCS_DetectVG1.1020.0201.124
BASiCS_DiagHist1.4870.0361.527
BASiCS_DiagPlot2.9630.0483.018
BASiCS_DivideAndConquer 3.032 0.11820.083
BASiCS_Draw0.3300.0040.354
BASiCS_EffectiveSize0.3490.0040.354
BASiCS_Filter0.0020.0000.003
BASiCS_LoadChain2.0000.0682.074
BASiCS_MCMC8.1910.0928.308
BASiCS_MockSCE0.2800.0030.285
BASiCS_PlotDE4.8240.0924.930
BASiCS_PlotOffset1.4120.0121.427
BASiCS_PlotVG0.4900.0040.495
BASiCS_PriorParam0.2210.0000.221
BASiCS_ShowFit0.3210.0000.322
BASiCS_Sim0.6000.0040.606
BASiCS_Summary-methods0.0050.0000.005
BASiCS_Summary1.9940.0602.060
BASiCS_TestDE9.6190.0569.701
BASiCS_VarThresholdSearchHVG_LVG2.8190.0362.861
BASiCS_VarianceDecomp0.2700.0000.271
Summary-BASiCS_Chain-method0.2690.0000.270
dim-BASiCS_Chain-method0.0020.0040.006
dimnames-BASiCS_Chain-method0.0060.0000.007
displayChainBASiCS-BASiCS_Chain-method0.1520.0140.217
displaySummaryBASiCS-BASiCS_Summary-method0.1450.0070.152
makeExampleBASiCS_Data0.2220.0000.223
newBASiCS_Chain3.8920.1164.018
plot-BASiCS_Chain-method0.1590.0030.161
plot-BASiCS_Summary-method0.1410.0060.148
show-BASiCS_ResultDE-method0.1430.0100.153
show-BASiCS_ResultVG-method0.1460.0030.149
show-BASiCS_ResultsDE-method0.1360.0130.150
subset-BASiCS_Chain-method1.3430.0051.351