Back to Build/check report for BioC 3.18:   simplified   long
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This page was generated on 2023-05-26 06:18:04 -0000 (Fri, 26 May 2023).

HostnameOSArch (*)R versionInstalled pkgs
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.3.0 (2023-04-21) -- "Already Tomorrow" 4254
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CHECK results for BASiCS on kunpeng2


To the developers/maintainers of the BASiCS package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BASiCS.git to reflect on this report. See Troubleshooting Build Report for more information.

- Use the following Renviron settings to reproduce errors and warnings.

Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details.

raw results

Package 127/2197HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BASiCS 2.13.0  (landing page)
Catalina Vallejos
Snapshot Date: 2023-05-25 13:29:39 -0000 (Thu, 25 May 2023)
git_url: https://git.bioconductor.org/packages/BASiCS
git_branch: devel
git_last_commit: 66cc677
git_last_commit_date: 2023-04-25 14:56:51 -0000 (Tue, 25 Apr 2023)
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  

Summary

Package: BASiCS
Version: 2.13.0
Command: /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:BASiCS.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings BASiCS_2.13.0.tar.gz
StartedAt: 2023-05-26 03:38:26 -0000 (Fri, 26 May 2023)
EndedAt: 2023-05-26 03:52:34 -0000 (Fri, 26 May 2023)
EllapsedTime: 847.2 seconds
RetCode: 0
Status:   OK  
CheckDir: BASiCS.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:BASiCS.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings BASiCS_2.13.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/BASiCS.Rcheck’
* using R version 4.3.0 (2023-04-21)
* 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
* checking for file ‘BASiCS/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BASiCS’ version ‘2.13.0’
* 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  10.6Mb
* 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                         user system elapsed
BASiCS_MCMC             9.764  0.064   9.845
BASiCS_TestDE           9.272  0.056   9.346
newBASiCS_Chain         5.936  0.036   5.982
BASiCS_Chain            5.622  0.020   5.652
BASiCS_DivideAndConquer 4.044  0.015  22.260
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘BASiCS.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

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



Installation output

BASiCS.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-4.3.0/bin/R CMD INSTALL BASiCS
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.3.0/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-4.3.0/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.0/library/RcppArmadillo/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -c BASiCS.cpp -o BASiCS.o
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.0/library/RcppArmadillo/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -shared -L/home/biocbuild/R/R-4.3.0/lib -L/usr/local/lib -o BASiCS.so BASiCS.o RcppExports.o -L/home/biocbuild/R/R-4.3.0/lib -lRlapack -L/home/biocbuild/R/R-4.3.0/lib -lRblas -lgfortran -lm -fopenmp -L/home/biocbuild/R/R-4.3.0/lib -lR
installing to /home/biocbuild/R/R-4.3.0/site-library/00LOCK-BASiCS/00new/BASiCS/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (BASiCS)

Tests output

BASiCS.Rcheck/tests/testthat.Rout


R version 4.3.0 (2023-04-21) -- "Already Tomorrow"
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: 0.013
system: 0
elapsed: 0.013

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

-------------------------------------------------------------
BASiCS version 2.13.0 : 
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 2.13.0 : 
vertical integration (spikes case) 
-------------------------------------------------------------

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

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

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

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

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

-------------------------------------------------------------
BASiCS version 2.13.0 : 
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 2.13.0 : 
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: 0.013
system: 0
elapsed: 0.013

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

-------------------------------------------------------------
BASiCS version 2.13.0 : 
vertical integration (spikes case) 
-------------------------------------------------------------

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

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

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

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

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

-------------------------------------------------------------
BASiCS version 2.13.0 : 
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: 0.012

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

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

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

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

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

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

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

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

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

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

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

-------------------------------------------------------------
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: 0.014
system: 0
elapsed: 0.014

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

-------------------------------------------------------------
BASiCS version 2.13.0 : 
vertical integration (spikes case) 
-------------------------------------------------------------

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

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

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

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

-------------------------------------------------------------
BASiCS version 2.13.0 : 
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: 0.008
system: 0
elapsed: 0.008

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

-------------------------------------------------------------
BASiCS version 2.13.0 : 
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 2.13.0 : 
vertical integration (spikes case) 
-------------------------------------------------------------

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

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

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

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

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

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

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

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

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

-------------------------------------------------------------
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: 0.011
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: 0.015
system: 0
elapsed: 0.015

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

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

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

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

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

-------------------------------------------------------------
BASiCS version 2.13.0 : 
vertical integration (spikes case) 
-------------------------------------------------------------

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

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

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

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

-------------------------------------------------------------
BASiCS version 2.13.0 : 
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: 0.069
system: 0
elapsed: 0.07

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

-------------------------------------------------------------
BASiCS version 2.13.0 : 
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: 0.059

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

-------------------------------------------------------------
BASiCS version 2.13.0 : 
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: 0.23
Average acceptance rate among mu[i]'s: 0.5172
Maximum acceptance rate among mu[i]'s: 0.83
 
 
Minimum acceptance rate among delta[i]'s: 0.51
Average acceptance rate among delta[i]'s: 0.6812
Maximum acceptance rate among delta[i]'s: 0.79
 
 
Minimum acceptance rate among nu[jk]'s: 0.82
Average acceptance rate among nu[jk]'s: 0.9568
Maximum acceptance rate among nu[jk]'s: 1
 
 
Minimum acceptance rate among theta[k]'s: 0.44
Average acceptance rate among theta[k]'s: 0.72
Maximum acceptance rate among theta[k]'s: 1
 
-----------------------------------------------------
 
-------------------------------------------------------------
MCMC running time 
-------------------------------------------------------------
user: 0.206
system: 0
elapsed: 0.206

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


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

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

-----------------------------------------------------
MCMC sampler has been started: 200 iterations to go.
-----------------------------------------------------
-----------------------------------------------------
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: 0.11
Average acceptance rate among mu[i]'s: 0.502
Maximum acceptance rate among mu[i]'s: 0.78
 
 
Minimum acceptance rate among delta[i]'s: 0.55
Average acceptance rate among delta[i]'s: 0.6778
Maximum acceptance rate among delta[i]'s: 0.83
 
 
Minimum acceptance rate among nu[jk]'s: 0.86
Average acceptance rate among nu[jk]'s: 0.9533
Maximum acceptance rate among nu[jk]'s: 1
 
 
Minimum acceptance rate among theta[k]'s: 0.4
Average acceptance rate among theta[k]'s: 0.685
Maximum acceptance rate among theta[k]'s: 0.97
 
-----------------------------------------------------
 
-------------------------------------------------------------
MCMC running time 
-------------------------------------------------------------
user: 0.201
system: 0.004
elapsed: 0.205

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

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: 0.008
system: 0
elapsed: 0.008

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

-------------------------------------------------------------
BASiCS version 2.13.0 : 
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: 0.004
elapsed: 0.011

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

-------------------------------------------------------------
BASiCS version 2.13.0 : 
vertical integration (spikes case) 
-------------------------------------------------------------

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

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

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

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

-------------------------------------------------------------
BASiCS version 2.13.0 : 
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 2.13.0 : 
vertical integration (spikes case) 
-------------------------------------------------------------

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

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

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

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

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

-------------------------------------------------------------
BASiCS version 2.13.0 : 
vertical integration (spikes case) 
-------------------------------------------------------------

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

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

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

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

-------------------------------------------------------------
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: 0.009
system: 0
elapsed: 0.01

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

-------------------------------------------------------------
MCMC running time 
-------------------------------------------------------------
user: 0.005
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: 0.01
system: 0
elapsed: 0.009

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

-------------------------------------------------------------
BASiCS version 2.13.0 : 
vertical integration (spikes case) 
-------------------------------------------------------------

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

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

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

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

-------------------------------------------------------------
BASiCS version 2.13.0 : 
vertical integration (spikes case) 
-------------------------------------------------------------

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

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

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

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

-------------------------------------------------------------
BASiCS version 2.13.0 : 
vertical integration (spikes case) 
-------------------------------------------------------------

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

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

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

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

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

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

-------------------------------------------------------------
BASiCS_Chain object stored as chain_.Rds file in
'/home/biocbuild/bbs-3.18-bioc/meat/BASiCS.Rcheck/tests/testthat' directory ... 
-------------------------------------------------------------

-------------------------------------------------------------
Storing trajectories of adaptive proposal variances (log-scale) aschain_ls_.Rds file in 
'/home/biocbuild/bbs-3.18-bioc/meat/BASiCS.Rcheck/tests/testthat' directory ... 
-------------------------------------------------------------

-------------------------------------------------------------
BASiCS version 2.13.0 : 
vertical integration (spikes case) 
-------------------------------------------------------------

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

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

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

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

-------------------------------------------------------------
BASiCS_Chain object stored as chain_.Rds file in
'/home/biocbuild/bbs-3.18-bioc/meat/BASiCS.Rcheck/tests/testthat' directory ... 
-------------------------------------------------------------

-------------------------------------------------------------
Storing trajectories of adaptive proposal variances (log-scale) aschain_ls_.Rds file in 
'/home/biocbuild/bbs-3.18-bioc/meat/BASiCS.Rcheck/tests/testthat' directory ... 
-------------------------------------------------------------

-------------------------------------------------------------
BASiCS version 2.13.0 : 
vertical integration (spikes case) 
-------------------------------------------------------------

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

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

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

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

-------------------------------------------------------------
BASiCS_Chain object stored as chain_.Rds file in
'/home/biocbuild/bbs-3.18-bioc/meat/BASiCS.Rcheck/tests/testthat' directory ... 
-------------------------------------------------------------

-------------------------------------------------------------
Storing trajectories of adaptive proposal variances (log-scale) aschain_ls_.Rds file in 
'/home/biocbuild/bbs-3.18-bioc/meat/BASiCS.Rcheck/tests/testthat' directory ... 
-------------------------------------------------------------

-------------------------------------------------------------
BASiCS version 2.13.0 : horizontal integration (no-spikes case)
-------------------------------------------------------------

Randomly, 1 out of 10
genes was left as reference at each iteration 
List of reference genes and frequencies stored as a .txt file in
'/home/biocbuild/bbs-3.18-bioc/meat/BASiCS.Rcheck/tests/testthat' directory ... 
-------------------------------------------------------------

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

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

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

-------------------------------------------------------------
BASiCS_Chain object stored as chain_.Rds file in
'/home/biocbuild/bbs-3.18-bioc/meat/BASiCS.Rcheck/tests/testthat' directory ... 
-------------------------------------------------------------

-------------------------------------------------------------
Storing trajectories of adaptive proposal variances (log-scale) aschain_ls_.Rds file in 
'/home/biocbuild/bbs-3.18-bioc/meat/BASiCS.Rcheck/tests/testthat' directory ... 
-------------------------------------------------------------

-------------------------------------------------------------
BASiCS version 2.13.0 : horizontal integration (no-spikes case)
-------------------------------------------------------------

Randomly, 1 out of 10
genes was left as reference at each iteration 
List of reference genes and frequencies stored as a .txt file in
'/home/biocbuild/bbs-3.18-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: 0.01
system: 0
elapsed: 0.011

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

-------------------------------------------------------------
BASiCS version 2.13.0 : 
vertical integration (spikes case) 
-------------------------------------------------------------

`BASiCS_Chain` class definition was outdated. 
Object updated to be compatible with BASiCS version 2.13.0.
Set 'StoreUpdatedChain' = TRUE to save updated object.

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

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

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

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

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

-------------------------------------------------------------
BASiCS version 2.13.0 : 
vertical integration (spikes case) 
-------------------------------------------------------------

`BASiCS_Chain` class definition was outdated. 
Object updated to be compatible with BASiCS version 2.13.0.
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: 0.024
system: 0
elapsed: 0.025

-------------------------------------------------------------
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'.
see ?scRNAseq and browseVignettes('scRNAseq') for documentation
loading from cache
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: 0.392
system: 0.004
elapsed: 0.396

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

-------------------------------------------------------------
BASiCS version 2.13.0 : 
vertical integration (spikes case) 
-------------------------------------------------------------

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

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

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

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

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

-------------------------------------------------------------
Storing trajectories of adaptive proposal variances (log-scale) aschain_ls_.Rds file in 
'/home/biocbuild/bbs-3.18-bioc/meat/BASiCS.Rcheck/tests/testthat' directory ... 
-------------------------------------------------------------

-------------------------------------------------------------
BASiCS version 2.13.0 : 
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: 0.393
system: 0
elapsed: 0.393

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

-------------------------------------------------------------
BASiCS version 2.13.0 : 
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: 0.334
system: 0
elapsed: 0.335

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

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

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

-------------------------------------------------------------
MCMC running time 
-------------------------------------------------------------
user: 0.331
system: 0.008
elapsed: 0.339

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

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

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

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

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

-------------------------------------------------------------
Storing trajectories of adaptive proposal variances (log-scale) aschain_ls_.Rds file in 
'/home/biocbuild/bbs-3.18-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: 0.335
system: 0.008
elapsed: 0.344

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

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

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

-------------------------------------------------------------
MCMC running time 
-------------------------------------------------------------
user: 0.34
system: 0.004
elapsed: 0.345

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

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

-------------------------------------------------------------
MCMC running time 
-------------------------------------------------------------
user: 0.431
system: 0
elapsed: 0.431

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

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

-------------------------------------------------------------
MCMC running time 
-------------------------------------------------------------
user: 0.431
system: 0.004
elapsed: 0.435

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

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

-------------------------------------------------------------
MCMC running time 
-------------------------------------------------------------
user: 0.023
system: 0
elapsed: 0.023

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

-------------------------------------------------------------
Storing trajectories of adaptive proposal variances (log-scale) aschain_ls_.Rds file in 
'/home/biocbuild/bbs-3.18-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: 0.496
system: 0
elapsed: 0.497

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

-------------------------------------------------------------
BASiCS version 2.13.0 : 
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 
-------------------------------------------------------------

-------------------------------------------------------------
Storing trajectories of adaptive proposal variances (log-scale) aschain_ls_.Rds file in 
'/home/biocbuild/bbs-3.18-bioc/meat/BASiCS.Rcheck/tests/testthat' directory ... 
-------------------------------------------------------------

-------------------------------------------------------------
BASiCS version 2.13.0 : 
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: 0.007
system: 0
elapsed: 0.008

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

-------------------------------------------------------------
BASiCS version 2.13.0 : 
vertical integration (spikes case) 
-------------------------------------------------------------

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

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

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

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

-------------------------------------------------------------
BASiCS version 2.13.0 : 
vertical integration (spikes case) 
-------------------------------------------------------------

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

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

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

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

-------------------------------------------------------------
BASiCS version 2.13.0 : 
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 2.13.0 : 
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: 0.005
system: 0
elapsed: 0.005

-------------------------------------------------------------
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: 0.01
system: 0
elapsed: 0.01

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

-------------------------------------------------------------
BASiCS version 2.13.0 : 
vertical integration (spikes case) 
-------------------------------------------------------------

[ FAIL 0 | WARN 0 | SKIP 0 | PASS 456 ]
> 
> proc.time()
   user  system elapsed 
324.223   7.627 367.436 

Example timings

BASiCS.Rcheck/BASiCS-Ex.timings

nameusersystemelapsed
BASiCS_Chain-methods3.3790.0043.388
BASiCS_Chain5.6220.0205.652
BASiCS_CorrectOffset0.0130.0040.017
BASiCS_DenoisedCounts3.5000.0443.550
BASiCS_DenoisedRates3.2500.0083.263
BASiCS_DetectVG1.0770.0641.143
BASiCS_DiagHist1.4040.0241.431
BASiCS_DiagPlot2.7340.0482.787
BASiCS_DivideAndConquer 4.044 0.01522.260
BASiCS_Draw0.5860.0040.591
BASiCS_EffectiveSize0.3000.0000.301
BASiCS_Filter0.0020.0000.003
BASiCS_LoadChain2.8870.0402.932
BASiCS_MCMC9.7640.0649.845
BASiCS_MockSCE0.5430.0030.548
BASiCS_PlotDE4.7160.0554.779
BASiCS_PlotOffset1.3530.0001.356
BASiCS_PlotVG0.5380.0040.543
BASiCS_PriorParam0.4480.0080.457
BASiCS_ShowFit0.3320.0000.332
BASiCS_Sim1.2400.0041.247
BASiCS_Summary-methods0.0050.0000.006
BASiCS_Summary3.0160.0243.045
BASiCS_TestDE9.2720.0569.346
BASiCS_VarThresholdSearchHVG_LVG3.1500.0123.166
BASiCS_VarianceDecomp0.3030.0000.303
Summary-BASiCS_Chain-method0.0730.0000.072
dim-BASiCS_Chain-method0.0070.0000.006
dimnames-BASiCS_Chain-method0.0060.0000.007
displayChainBASiCS-BASiCS_Chain-method0.1520.0200.257
displaySummaryBASiCS-BASiCS_Summary-method0.1410.0090.151
makeExampleBASiCS_Data0.4490.0000.450
newBASiCS_Chain5.9360.0365.982
plot-BASiCS_Chain-method0.1330.0110.145
plot-BASiCS_Summary-method0.1400.0000.141
show-BASiCS_ResultDE-method0.1370.0040.141
show-BASiCS_ResultVG-method0.1420.0000.141
show-BASiCS_ResultsDE-method0.1300.0120.141
subset-BASiCS_Chain-method1.2930.0401.335