##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:BASiCS.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings BASiCS_2.18.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/BASiCS.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘BASiCS/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BASiCS’ version ‘2.18.0’
* 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++ (Ubuntu 13.2.0-23ubuntu4) 13.2.0’
* checking C++ specification ... NOTE
  Specified C++11: please drop specification unless essential
* checking installed package size ... NOTE
  installed size is 11.3Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   8.4Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                         user system elapsed
BASiCS_MCMC             5.280  0.008   5.299
BASiCS_DivideAndConquer 3.157  0.016  14.125
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/BASiCS.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL BASiCS
###
##############################################################################
##############################################################################


* installing to library ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘BASiCS’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 13.2.0-23ubuntu4) 13.2.0’
using C++11
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/RcppArmadillo/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall  -c BASiCS.cpp -o BASiCS.o
In file included from /home/biocbuild/bbs-3.20-bioc/R/include/R.h:73,
                 from libraries.h:6,
                 from utils.h:4,
                 from updates.h:4,
                 from BASiCS.cpp:1:
/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include/Rcpp/exceptions/cpp11/exceptions.h: In function ‘void Rcpp::Rf_warning(const char*, Args&& ...) [with Args = {const char*}]’:
/home/biocbuild/bbs-3.20-bioc/R/include/R_ext/Error.h:69:17: warning: infinite recursion detected [-Winfinite-recursion]
   69 | #define warning Rf_warning
      |                 ^~~~~~~~~~
/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include/Rcpp/exceptions/cpp11/exceptions.h:46:13: note: in expansion of macro ‘warning’
   46 | inline void warning(const char* fmt, Args&&... args ) {
      |             ^~~~~~~
In file included from /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include/Rcpp/exceptions.h:180,
                 from /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include/RcppCommon.h:130,
                 from /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:25,
                 from /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/RcppArmadillo/include/RcppArmadillo.h:29,
                 from libraries.h:11:
/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include/Rcpp/exceptions/cpp11/exceptions.h:47:15: note: recursive call
   47 |     Rf_warning("%s", tfm::format(fmt, std::forward<Args>(args)... ).c_str());
      |     ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/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/bbs-3.20-bioc/R/lib -L/usr/local/lib -o BASiCS.so BASiCS.o RcppExports.o -llapack -L/home/biocbuild/bbs-3.20-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -fopenmp -L/home/biocbuild/bbs-3.20-bioc/R/lib -lR
installing to /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/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 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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

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

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

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

Attaching package: 'MatrixGenerics'

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

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

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

Attaching package: 'BiocGenerics'

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

    IQR, mad, sd, var, xtabs

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

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, saveRDS, setdiff, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    findMatches

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

    I, expand.grid, unname

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

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


Attaching package: 'Biobase'

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

    rowMedians

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

    anyMissing, rowMedians

    Welcome to 'BASiCS'. If you used 'BASiCS' before its release in
    Bioconductor, please visit:
    https://github.com/catavallejos/BASiCS/wiki.
> 
> test_check("BASiCS")
-------------------------------------------------------------
Log-fold change thresholds are now set in a log2 scale. 
Original BASiCS release used a natural logarithm scale.
-------------------------------------------------------------
Offset estimate: 0.6714
(ratio SC vs P&S).
-------------------------------------------------------------

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

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

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

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

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

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

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

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

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

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

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

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

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

-------------------------------------------------------------
MCMC running time 
-------------------------------------------------------------
user: 0.008
system: 0.001
elapsed: 0.009

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

-------------------------------------------------------------
BASiCS version 2.18.0 : 
vertical integration (spikes case) 
-------------------------------------------------------------

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

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

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

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

-------------------------------------------------------------
BASiCS version 2.18.0 : 
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: 0.008
system: 0
elapsed: 0.008

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

-------------------------------------------------------------
BASiCS version 2.18.0 : 
vertical integration (spikes case) 
-------------------------------------------------------------

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

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

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

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

-------------------------------------------------------------
BASiCS version 2.18.0 : 
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 2.18.0 : 
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: 0.006

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

-------------------------------------------------------------
BASiCS version 2.18.0 : 
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: 0.008
system: 0
elapsed: 0.008

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

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

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

-------------------------------------------------------------
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: 0.007

-------------------------------------------------------------
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: 0.005
system: 0
elapsed: 0.005

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

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

-------------------------------------------------------------
BASiCS version 2.18.0 : 
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 2.18.0 : 
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: 0.005
system: 0
elapsed: 0.005

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

-------------------------------------------------------------
BASiCS version 2.18.0 : 
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: 0.008
system: 0
elapsed: 0.008

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

-------------------------------------------------------------
BASiCS version 2.18.0 : 
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: 0.007
system: 0
elapsed: 0.008

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

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

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

-------------------------------------------------------------
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: 0.005
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: 0.007
system: 0
elapsed: 0.006

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

-------------------------------------------------------------
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: 0.033
system: 0
elapsed: 0.033

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

-------------------------------------------------------------
BASiCS version 2.18.0 : 
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: 0.033
system: 0
elapsed: 0.032

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

-------------------------------------------------------------
BASiCS version 2.18.0 : 
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: 0.034
system: 0.001
elapsed: 0.034

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

-------------------------------------------------------------
BASiCS version 2.18.0 : 
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: 0.029
system: 0
elapsed: 0.029

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

-------------------------------------------------------------
BASiCS version 2.18.0 : 
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: 43
RefGene: 43
RefGene: 15
RefGene: 11
RefGene: 13
RefGene: 17
RefGene: 15
RefGene: 13
RefGene: 31
RefGene: 0
RefGene: 15
RefGene: 43
RefGene: 11
RefGene: 0
RefGene: 0
RefGene: 39
RefGene: 44
RefGene: 39
RefGene: 11
RefGene: 0
RefGene: 13
RefGene: 11
RefGene: 15
RefGene: 44
RefGene: 13
RefGene: 16
RefGene: 44
RefGene: 39
RefGene: 0
RefGene: 0
RefGene: 17
RefGene: 11
RefGene: 11
RefGene: 13
RefGene: 13
RefGene: 31
RefGene: 44
RefGene: 31
RefGene: 39
RefGene: 39
RefGene: 16
RefGene: 31
RefGene: 43
RefGene: 16
RefGene: 43
RefGene: 43
RefGene: 11
RefGene: 39
RefGene: 13
RefGene: 16
RefGene: 13
RefGene: 17
RefGene: 31
RefGene: 11
RefGene: 15
RefGene: 0
RefGene: 44
RefGene: 13
RefGene: 17
RefGene: 31
RefGene: 13
RefGene: 43
RefGene: 31
RefGene: 31
RefGene: 39
RefGene: 11
RefGene: 31
RefGene: 16
RefGene: 13
RefGene: 11
RefGene: 13
RefGene: 0
RefGene: 11
RefGene: 31
RefGene: 17
RefGene: 31
RefGene: 44
RefGene: 16
RefGene: 44
RefGene: 0
RefGene: 13
RefGene: 11
RefGene: 31
RefGene: 16
RefGene: 0
RefGene: 0
RefGene: 15
RefGene: 44
RefGene: 44
RefGene: 43
RefGene: 39
RefGene: 44
RefGene: 15
RefGene: 15
RefGene: 43
RefGene: 16
RefGene: 15
RefGene: 17
RefGene: 17
RefGene: 31
-----------------------------------------------------
End of Burn-in period.
-----------------------------------------------------
RefGene: 0
RefGene: 15
RefGene: 39
RefGene: 17
RefGene: 17
RefGene: 16
RefGene: 44
RefGene: 44
RefGene: 44
RefGene: 44
RefGene: 44
RefGene: 44
RefGene: 16
RefGene: 43
RefGene: 11
RefGene: 31
RefGene: 39
RefGene: 13
RefGene: 31
RefGene: 17
RefGene: 44
RefGene: 15
RefGene: 17
RefGene: 39
RefGene: 11
RefGene: 16
RefGene: 11
RefGene: 16
RefGene: 11
RefGene: 16
RefGene: 15
RefGene: 17
RefGene: 17
RefGene: 31
RefGene: 17
RefGene: 17
RefGene: 31
RefGene: 11
RefGene: 17
RefGene: 15
RefGene: 0
RefGene: 31
RefGene: 43
RefGene: 15
RefGene: 11
RefGene: 0
RefGene: 15
RefGene: 0
RefGene: 16
RefGene: 43
RefGene: 44
RefGene: 11
RefGene: 43
RefGene: 16
RefGene: 15
RefGene: 15
RefGene: 31
RefGene: 39
RefGene: 31
RefGene: 39
RefGene: 0
RefGene: 16
RefGene: 15
RefGene: 43
RefGene: 16
RefGene: 39
RefGene: 17
RefGene: 17
RefGene: 31
RefGene: 17
RefGene: 11
RefGene: 13
RefGene: 17
RefGene: 11
RefGene: 16
RefGene: 31
RefGene: 15
RefGene: 43
RefGene: 44
RefGene: 39
RefGene: 0
RefGene: 11
RefGene: 39
RefGene: 0
RefGene: 39
RefGene: 16
RefGene: 16
RefGene: 11
RefGene: 44
RefGene: 0
RefGene: 13
RefGene: 13
RefGene: 0
RefGene: 15
RefGene: 15
RefGene: 13
RefGene: 17
RefGene: 15
RefGene: 43
RefGene: 15
 
-----------------------------------------------------
-----------------------------------------------------
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: 0.4964
Maximum acceptance rate among mu[i]'s: 0.79
 
 
Minimum acceptance rate among delta[i]'s: 0.55
Average acceptance rate among delta[i]'s: 0.6742
Maximum acceptance rate among delta[i]'s: 0.82
 
 
Minimum acceptance rate among nu[jk]'s: 0.85
Average acceptance rate among nu[jk]'s: 0.9525
Maximum acceptance rate among nu[jk]'s: 1
 
 
Minimum acceptance rate among theta[k]'s: 0.03
Average acceptance rate among theta[k]'s: 0.515
Maximum acceptance rate among theta[k]'s: 1
 
-----------------------------------------------------
 
-------------------------------------------------------------
MCMC running time 
-------------------------------------------------------------
user: 0.097
system: 0
elapsed: 0.096

-------------------------------------------------------------
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: 11
RefGene: 22
RefGene: 14
RefGene: 10
RefGene: 11
RefGene: 22
RefGene: 47
RefGene: 23
RefGene: 23
RefGene: 23
RefGene: 11
RefGene: 47
RefGene: 14
RefGene: 11
RefGene: 19
RefGene: 11
RefGene: 47
RefGene: 36
RefGene: 47
RefGene: 22
RefGene: 47
RefGene: 22
RefGene: 9
RefGene: 9
RefGene: 9
RefGene: 36
RefGene: 11
RefGene: 10
RefGene: 47
RefGene: 11
RefGene: 36
RefGene: 19
RefGene: 36
RefGene: 19
RefGene: 22
RefGene: 36
RefGene: 11
RefGene: 23
RefGene: 10
RefGene: 23
RefGene: 14
RefGene: 22
RefGene: 9
RefGene: 11
RefGene: 14
RefGene: 23
RefGene: 47
RefGene: 10
RefGene: 9
RefGene: 47
RefGene: 9
RefGene: 47
RefGene: 23
RefGene: 9
RefGene: 49
RefGene: 10
RefGene: 49
RefGene: 23
RefGene: 19
RefGene: 23
RefGene: 49
RefGene: 22
RefGene: 11
RefGene: 9
RefGene: 14
RefGene: 11
RefGene: 9
RefGene: 10
RefGene: 36
RefGene: 47
RefGene: 10
RefGene: 23
RefGene: 10
RefGene: 14
RefGene: 14
RefGene: 22
RefGene: 19
RefGene: 19
RefGene: 11
RefGene: 23
RefGene: 47
RefGene: 36
RefGene: 49
RefGene: 47
RefGene: 19
RefGene: 36
RefGene: 36
RefGene: 47
RefGene: 22
RefGene: 49
RefGene: 49
RefGene: 49
RefGene: 22
RefGene: 14
RefGene: 49
RefGene: 9
RefGene: 49
RefGene: 49
RefGene: 22
RefGene: 19
-----------------------------------------------------
End of Burn-in period.
-----------------------------------------------------
RefGene: 19
RefGene: 19
RefGene: 9
RefGene: 10
RefGene: 47
RefGene: 9
RefGene: 11
RefGene: 14
RefGene: 9
RefGene: 11
RefGene: 11
RefGene: 47
RefGene: 10
RefGene: 14
RefGene: 14
RefGene: 14
RefGene: 47
RefGene: 9
RefGene: 49
RefGene: 10
RefGene: 36
RefGene: 47
RefGene: 9
RefGene: 22
RefGene: 36
RefGene: 14
RefGene: 22
RefGene: 14
RefGene: 19
RefGene: 36
RefGene: 22
RefGene: 19
RefGene: 47
RefGene: 14
RefGene: 14
RefGene: 23
RefGene: 22
RefGene: 19
RefGene: 9
RefGene: 47
RefGene: 14
RefGene: 22
RefGene: 10
RefGene: 14
RefGene: 19
RefGene: 47
RefGene: 9
RefGene: 47
RefGene: 47
RefGene: 47
RefGene: 14
RefGene: 19
RefGene: 23
RefGene: 36
RefGene: 19
RefGene: 49
RefGene: 23
RefGene: 36
RefGene: 36
RefGene: 11
RefGene: 11
RefGene: 19
RefGene: 36
RefGene: 11
RefGene: 22
RefGene: 23
RefGene: 14
RefGene: 22
RefGene: 10
RefGene: 47
RefGene: 47
RefGene: 14
RefGene: 10
RefGene: 47
RefGene: 22
RefGene: 19
RefGene: 11
RefGene: 47
RefGene: 9
RefGene: 23
RefGene: 47
RefGene: 10
RefGene: 22
RefGene: 49
RefGene: 49
RefGene: 47
RefGene: 14
RefGene: 9
RefGene: 10
RefGene: 47
RefGene: 36
RefGene: 19
RefGene: 11
RefGene: 14
RefGene: 49
RefGene: 22
RefGene: 14
RefGene: 10
RefGene: 14
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: 0.22
Average acceptance rate among mu[i]'s: 0.5086
Maximum acceptance rate among mu[i]'s: 0.77
 
 
Minimum acceptance rate among delta[i]'s: 0.52
Average acceptance rate among delta[i]'s: 0.67
Maximum acceptance rate among delta[i]'s: 0.76
 
 
Minimum acceptance rate among nu[jk]'s: 0.83
Average acceptance rate among nu[jk]'s: 0.96
Maximum acceptance rate among nu[jk]'s: 1
 
 
Minimum acceptance rate among theta[k]'s: 0.57
Average acceptance rate among theta[k]'s: 0.725
Maximum acceptance rate among theta[k]'s: 0.88
 
-----------------------------------------------------
 
-------------------------------------------------------------
MCMC running time 
-------------------------------------------------------------
user: 0.099
system: 0
elapsed: 0.1

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


Combining batch posteriors for nu
Combining batch posteriors for theta

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

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: 0.004
system: 0
elapsed: 0.004

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

-------------------------------------------------------------
BASiCS version 2.18.0 : 
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: 0.006

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

-------------------------------------------------------------
BASiCS version 2.18.0 : 
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: 0.007

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

-------------------------------------------------------------
BASiCS version 2.18.0 : 
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: 0.004
system: 0
elapsed: 0.004

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

-------------------------------------------------------------
BASiCS version 2.18.0 : 
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: 0.003
system: 0
elapsed: 0.003

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

-------------------------------------------------------------
BASiCS version 2.18.0 : 
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: 0.006
system: 0
elapsed: 0.006

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

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

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

-------------------------------------------------------------
MCMC running time 
-------------------------------------------------------------
user: 0.004
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: 0.003
system: 0
elapsed: 0.003

-------------------------------------------------------------
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: 0.003
system: 0
elapsed: 0.002

-------------------------------------------------------------
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: 0.003
system: 0
elapsed: 0.002

-------------------------------------------------------------
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: 0.004
system: 0
elapsed: 0.004

-------------------------------------------------------------
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: 0.003
system: 0
elapsed: 0.003

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

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

-------------------------------------------------------------
MCMC running time 
-------------------------------------------------------------
user: 0.004
system: 0
elapsed: 0.003

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

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

-------------------------------------------------------------
MCMC running time 
-------------------------------------------------------------
user: 0.323
system: 0
elapsed: 0.324

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

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

-------------------------------------------------------------
MCMC running time 
-------------------------------------------------------------
user: 0.004
system: 0
elapsed: 0.003

-------------------------------------------------------------
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: 0.005
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: 0.005
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: 0.004
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. 

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 2.18.0 : 
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: 0.004
system: 0
elapsed: 0.004

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

-------------------------------------------------------------
BASiCS version 2.18.0 : 
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: 0.005
system: 0
elapsed: 0.005

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

-------------------------------------------------------------
BASiCS version 2.18.0 : 
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: 0.004
system: 0
elapsed: 0.005

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

-------------------------------------------------------------
BASiCS_Chain object stored as chain_.Rds file in
'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/BASiCS.Rcheck/tests/testthat' directory ... 
-------------------------------------------------------------

-------------------------------------------------------------
Storing trajectories of adaptive proposal variances (log-scale) aschain_ls_.Rds file in 
'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/BASiCS.Rcheck/tests/testthat' directory ... 
-------------------------------------------------------------

-------------------------------------------------------------
BASiCS version 2.18.0 : 
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_Chain object stored as chain_.Rds file in
'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/BASiCS.Rcheck/tests/testthat' directory ... 
-------------------------------------------------------------

-------------------------------------------------------------
Storing trajectories of adaptive proposal variances (log-scale) aschain_ls_.Rds file in 
'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/BASiCS.Rcheck/tests/testthat' directory ... 
-------------------------------------------------------------

-------------------------------------------------------------
BASiCS version 2.18.0 : 
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: 0.005
system: 0
elapsed: 0.004

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

-------------------------------------------------------------
BASiCS_Chain object stored as chain_.Rds file in
'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/BASiCS.Rcheck/tests/testthat' directory ... 
-------------------------------------------------------------

-------------------------------------------------------------
Storing trajectories of adaptive proposal variances (log-scale) aschain_ls_.Rds file in 
'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/BASiCS.Rcheck/tests/testthat' directory ... 
-------------------------------------------------------------

-------------------------------------------------------------
BASiCS version 2.18.0 : 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
'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/BASiCS.Rcheck/tests/testthat' directory ... 
-------------------------------------------------------------

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

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

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

-------------------------------------------------------------
BASiCS_Chain object stored as chain_.Rds file in
'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/BASiCS.Rcheck/tests/testthat' directory ... 
-------------------------------------------------------------

-------------------------------------------------------------
Storing trajectories of adaptive proposal variances (log-scale) aschain_ls_.Rds file in 
'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/BASiCS.Rcheck/tests/testthat' directory ... 
-------------------------------------------------------------

-------------------------------------------------------------
BASiCS version 2.18.0 : 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
'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/BASiCS.Rcheck/tests/testthat' directory ... 
-------------------------------------------------------------

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

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

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

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

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

-------------------------------------------------------------
BASiCS version 2.18.0 : 
vertical integration (spikes case) 
-------------------------------------------------------------

`BASiCS_Chain` class definition was outdated. 
Object updated to be compatible with BASiCS version 2.18.0.
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: 0.008
system: 0
elapsed: 0.008

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

-------------------------------------------------------------
BASiCS version 2.18.0 : 
vertical integration (spikes case) 
-------------------------------------------------------------

`BASiCS_Chain` class definition was outdated. 
Object updated to be compatible with BASiCS version 2.18.0.
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: 0.013
system: 0
elapsed: 0.013

-------------------------------------------------------------
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: 0.193
system: 0.001
elapsed: 0.194

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

-------------------------------------------------------------
BASiCS version 2.18.0 : 
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 
'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/BASiCS.Rcheck/tests/testthat' directory ... 
-------------------------------------------------------------

-------------------------------------------------------------
BASiCS version 2.18.0 : 
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: 0.194
system: 0
elapsed: 0.195

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

-------------------------------------------------------------
BASiCS version 2.18.0 : 
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: 0.402
system: 0.004
elapsed: 0.406

-------------------------------------------------------------
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: 0.165
system: 0.001
elapsed: 0.165

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

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

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

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

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

-------------------------------------------------------------
Storing trajectories of adaptive proposal variances (log-scale) aschain_ls_.Rds file in 
'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/BASiCS.Rcheck/tests/testthat' directory ... 
-------------------------------------------------------------

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

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

-------------------------------------------------------------
MCMC running time 
-------------------------------------------------------------
user: 0.173
system: 0.001
elapsed: 0.177

-------------------------------------------------------------
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: 0.174
system: 0.001
elapsed: 0.175

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

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

-------------------------------------------------------------
MCMC running time 
-------------------------------------------------------------
user: 0.294
system: 0
elapsed: 0.295

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

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

-------------------------------------------------------------
MCMC running time 
-------------------------------------------------------------
user: 0.292
system: 0.002
elapsed: 0.295

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

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

-------------------------------------------------------------
MCMC running time 
-------------------------------------------------------------
user: 0.015
system: 0
elapsed: 0.015

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

-------------------------------------------------------------
Storing trajectories of adaptive proposal variances (log-scale) aschain_ls_.Rds file in 
'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/BASiCS.Rcheck/tests/testthat' directory ... 
-------------------------------------------------------------

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

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

-------------------------------------------------------------
MCMC running time 
-------------------------------------------------------------
user: 0.246
system: 0.002
elapsed: 0.248

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

-------------------------------------------------------------
BASiCS version 2.18.0 : 
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: 0.005
system: 0
elapsed: 0.005

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

-------------------------------------------------------------
Storing trajectories of adaptive proposal variances (log-scale) aschain_ls_.Rds file in 
'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/BASiCS.Rcheck/tests/testthat' directory ... 
-------------------------------------------------------------

-------------------------------------------------------------
BASiCS version 2.18.0 : 
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: 0.009
system: 0
elapsed: 0.009

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

-------------------------------------------------------------
BASiCS version 2.18.0 : 
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: 0.004
system: 0
elapsed: 0.004

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

-------------------------------------------------------------
BASiCS version 2.18.0 : 
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: 0.004
system: 0
elapsed: 0.005

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

-------------------------------------------------------------
BASiCS version 2.18.0 : 
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: 0.004
system: 0
elapsed: 0.005

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

-------------------------------------------------------------
BASiCS version 2.18.0 : 
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: 0.008

-------------------------------------------------------------
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: 0.004
system: 0
elapsed: 0.004

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

-------------------------------------------------------------
BASiCS version 2.18.0 : 
vertical integration (spikes case) 
-------------------------------------------------------------

[ FAIL 0 | WARN 0 | SKIP 0 | PASS 459 ]
> 
> proc.time()
   user  system elapsed 
180.854   2.062 204.844