##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:BASiCS.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings BASiCS_2.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/BASiCS.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (GCC) 10.3.1
    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 ‘2.14.0’
* 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 13.6Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs  10.7Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* 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 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 ... ERROR
Running examples in ‘BASiCS-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: BASiCS_VarianceDecomp
> ### Title: Decomposition of gene expression variability according to BASiCS
> ### Aliases: BASiCS_VarianceDecomp
> 
> ### ** Examples
> 
> 
> # For illustration purposes we load a built-in 'BASiCS_Chain' object
> # (obtained using the 'BASiCS_MCMC' function)
> data(ChainSC)
> 
> VD <- BASiCS_VarianceDecomp(ChainSC)
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’/home/biocbuild/R/R-4.3.1/bin/BATCH: line 60: 386927 Killed                  ${R_HOME}/bin/R -f ${in} ${opts} ${R_BATCH_OPTIONS} > ${out} 2>&1

 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
   
  -----------------------------------------------------
   
  -------------------------------------------------------------
  MCMC running time 
  -------------------------------------------------------------
  user: 0.206
  system: 0.004
  elapsed: 0.212
  
  -------------------------------------------------------------
  Output 
  -------------------------------------------------------------
  
  
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 ERRORs, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/BASiCS.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-4.3.1/bin/R CMD INSTALL BASiCS
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.3.1/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-4.3.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/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-4.3.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/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-4.3.1/lib -L/usr/local/lib -o BASiCS.so BASiCS.o RcppExports.o -llapack -lblas -lgfortran -lm -fopenmp -L/home/biocbuild/R/R-4.3.1/lib -lR
installing to /home/biocbuild/R/R-4.3.1/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)

R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

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

Attaching package: 'MatrixGenerics'

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

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

Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics

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, sort, 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: 0.014
system: 0
elapsed: 0.018

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

-------------------------------------------------------------
BASiCS version 2.14.0 : 
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 2.14.0 : 
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: 0.013

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

-------------------------------------------------------------
BASiCS version 2.14.0 : 
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 2.14.0 : 
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: 0.013

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

-------------------------------------------------------------
BASiCS version 2.14.0 : 
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: 0.019
system: 0.743
elapsed: 1.305

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

-------------------------------------------------------------
BASiCS version 2.14.0 : 
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: 0.013

-------------------------------------------------------------
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: 0.009
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: 0.01
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: 0.016

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

-------------------------------------------------------------
BASiCS version 2.14.0 : 
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: 0.012

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

-------------------------------------------------------------
BASiCS version 2.14.0 : 
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: 0.009
system: 0
elapsed: 0.009

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

-------------------------------------------------------------
BASiCS version 2.14.0 : 
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: 0.012
system: 0
elapsed: 0.012

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

-------------------------------------------------------------
BASiCS version 2.14.0 : 
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: 0.012
system: 0
elapsed: 0.012

-------------------------------------------------------------
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: 0.012

-------------------------------------------------------------
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: 0.065
system: 0
elapsed: 0.066

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

-------------------------------------------------------------
BASiCS version 2.14.0 : 
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: 0.068
system: 0
elapsed: 0.067

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

-------------------------------------------------------------
BASiCS version 2.14.0 : 
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: 0.099
system: 0.413
elapsed: 1.937

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

-------------------------------------------------------------
BASiCS version 2.14.0 : 
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 2.14.0 : 
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.
-----------------------------------------------------
-----------------------------------------------------
End of Burn-in period.
-----------------------------------------------------
 
-----------------------------------------------------
-----------------------------------------------------
All 200 MCMC iterations have been completed.
-----------------------------------------------------
-----------------------------------------------------
 
-----------------------------------------------------
Please see below a summary of the overall acceptance rates.
-----------------------------------------------------
 
Minimum acceptance rate among mu[i]'s: 0.15
Average acceptance rate among mu[i]'s: 0.5048
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: 0.6734
Maximum acceptance rate among delta[i]'s: 0.83
 
 
Minimum acceptance rate among nu[jk]'s: 0.82
Average acceptance rate among nu[jk]'s: 0.9536
Maximum acceptance rate among nu[jk]'s: 1
 
 
Minimum acceptance rate among theta[k]'s: 0.75
Average acceptance rate among theta[k]'s: 0.875
Maximum acceptance rate among theta[k]'s: 1
 
-----------------------------------------------------
 
-------------------------------------------------------------
MCMC running time 
-------------------------------------------------------------
user: 0.204
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.
-----------------------------------------------------
-----------------------------------------------------
End of Burn-in period.
-----------------------------------------------------
 
-----------------------------------------------------
-----------------------------------------------------
All 200 MCMC iterations have been completed.
-----------------------------------------------------
-----------------------------------------------------
 
-----------------------------------------------------
Please see below a summary of the overall acceptance rates.
-----------------------------------------------------
 
Minimum acceptance rate among mu[i]'s: 0.17
Average acceptance rate among mu[i]'s: 0.514
Maximum acceptance rate among mu[i]'s: 0.75
 
 
Minimum acceptance rate among delta[i]'s: 0.51
Average acceptance rate among delta[i]'s: 0.6766
Maximum acceptance rate among delta[i]'s: 0.8
 
 
Minimum acceptance rate among nu[jk]'s: 0.87
Average acceptance rate among nu[jk]'s: 0.957
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: 0.206
system: 0.004
elapsed: 0.212

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