Back to Multiple platform build/check report for BioC 3.6
A[B]CDEFGHIJKLMNOPQRSTUVWXYZ

CHECK report for BASiCS on tokay1

This page was generated on 2018-04-12 13:30:33 -0400 (Thu, 12 Apr 2018).

Package 93/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BASiCS 1.0.1
Catalina A. Vallejos
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/BASiCS
Branch: RELEASE_3_6
Last Commit: dba7914
Last Changed Date: 2018-03-18 15:01:01 -0400 (Sun, 18 Mar 2018)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: BASiCS
Version: 1.0.1
Command: rm -rf BASiCS.buildbin-libdir BASiCS.Rcheck && mkdir BASiCS.buildbin-libdir BASiCS.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=BASiCS.buildbin-libdir BASiCS_1.0.1.tar.gz >BASiCS.Rcheck\00install.out 2>&1 && cp BASiCS.Rcheck\00install.out BASiCS-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=BASiCS.buildbin-libdir --install="check:BASiCS-install.out" --force-multiarch --no-vignettes --timings BASiCS_1.0.1.tar.gz
StartedAt: 2018-04-11 22:21:45 -0400 (Wed, 11 Apr 2018)
EndedAt: 2018-04-11 22:28:09 -0400 (Wed, 11 Apr 2018)
EllapsedTime: 384.0 seconds
RetCode: 0
Status:  OK  
CheckDir: BASiCS.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf BASiCS.buildbin-libdir BASiCS.Rcheck && mkdir BASiCS.buildbin-libdir BASiCS.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=BASiCS.buildbin-libdir BASiCS_1.0.1.tar.gz >BASiCS.Rcheck\00install.out 2>&1 && cp BASiCS.Rcheck\00install.out BASiCS-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=BASiCS.buildbin-libdir --install="check:BASiCS-install.out" --force-multiarch --no-vignettes --timings BASiCS_1.0.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/BASiCS.Rcheck'
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'BASiCS/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'BASiCS' version '1.0.1'
* 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 whether package 'BASiCS' can be installed ... OK
* checking installed package size ... OK
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 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 compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.6-bioc/meat/BASiCS.buildbin-libdir/BASiCS/libs/i386/BASiCS.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
BASiCS_DenoisedCounts 7.90   0.02    7.93
BASiCS_DenoisedRates  7.85   0.00    7.84
BASiCS_MCMC           6.59   0.14    7.13
BASiCS_D_TestDE       0.19   0.05    5.18
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
BASiCS_MCMC           7.84   0.08    7.97
BASiCS_DenoisedRates  7.47   0.00    7.47
BASiCS_DenoisedCounts 6.92   0.00    6.93
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  Running 'testthat.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/BASiCS.Rcheck/00check.log'
for details.



Installation output

BASiCS.Rcheck/00install.out


install for i386

* installing *source* package 'BASiCS' ...
** libs
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/RcppArmadillo/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c BASiCS_CPPcode.cpp -o BASiCS_CPPcode.o
BASiCS_CPPcode.cpp: In function 'arma::mat muUpdateNoSpikes(const vec&, const vec&, const double&, const mat&, const vec&, const vec&, const vec&, const double&, const int&, const int&, arma::vec&, arma::vec&, const int&, const uvec&, const uvec&, const int&)':
BASiCS_CPPcode.cpp:1226:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (int i=0; i < ConstrainGene.size(); i++)
                   ^
BASiCS_CPPcode.cpp:1251:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int i=0; i < NotConstrainGene.size(); i++)
                     ^
BASiCS_CPPcode.cpp: In function 'Rcpp::List HiddenBASiCS_MCMCcppNoSpikes(int, int, int, Rcpp::NumericMatrix, Rcpp::NumericMatrix, Rcpp::NumericVector, Rcpp::NumericVector, Rcpp::NumericVector, Rcpp::NumericVector, double, double, double, double, double, double, double, double, double, Rcpp::NumericVector, Rcpp::NumericVector, Rcpp::NumericVector, double, Rcpp::NumericVector, Rcpp::NumericVector, int, int, int, double, double, Rcpp::NumericVector, Rcpp::NumericVector, Rcpp::NumericVector, Rcpp::NumericVector, double, Rcpp::NumericVector, int, Rcpp::NumericVector, Rcpp::NumericVector, Rcpp::NumericVector, int)':
BASiCS_CPPcode.cpp:1648:14: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
     if(i%Thin==0 & i>=Burn)
              ^
BASiCS_CPPcode.cpp:1666:19: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
     if(i%(2*Thin) == 0 & PrintProgress == 1)
                   ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/RcppArmadillo/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o BASiCS.dll tmp.def BASiCS_CPPcode.o RcppExports.o -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/i386 -lRlapack -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/i386 -lRblas -lgfortran -lm -lquadmath -LC:/local323/lib/i386 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/BASiCS.buildbin-libdir/BASiCS/libs/i386
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'BASiCS'
    finding HTML links ... done
    BASiCS_Chain-methods                    html  
    BASiCS_Chain                            html  
    BASiCS_D_TestDE                         html  
    BASiCS_DenoisedCounts                   html  
    finding level-2 HTML links ... done

    BASiCS_DenoisedRates                    html  
    BASiCS_DetectHVG_LVG                    html  
    BASiCS_Filter                           html  
    BASiCS_LoadChain                        html  
    BASiCS_MCMC                             html  
    BASiCS_Sim                              html  
    BASiCS_Summary-methods                  html  
    BASiCS_Summary                          html  
    BASiCS_TestDE                           html  
    BASiCS_VarThresholdSearchHVG_LVG        html  
    BASiCS_VarianceDecomp                   html  
    ChainRNA                                html  
    ChainSC                                 html  
    Summary-BASiCS_Chain-method             html  
    displayChainBASiCS-BASiCS_Chain-method
                                            html  
    displaySummaryBASiCS-BASiCS_Summary-method
                                            html  
    makeExampleBASiCS_Data                  html  
    newBASiCS_Chain                         html  
    newBASiCS_Data                          html  
    plot-BASiCS_Chain-method                html  
    plot-BASiCS_Summary-method              html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'BASiCS' ...
** libs
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/RcppArmadillo/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c BASiCS_CPPcode.cpp -o BASiCS_CPPcode.o
BASiCS_CPPcode.cpp: In function 'arma::mat muUpdateNoSpikes(const vec&, const vec&, const double&, const mat&, const vec&, const vec&, const vec&, const double&, const int&, const int&, arma::vec&, arma::vec&, const int&, const uvec&, const uvec&, const int&)':
BASiCS_CPPcode.cpp:1226:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (int i=0; i < ConstrainGene.size(); i++)
                   ^
BASiCS_CPPcode.cpp:1251:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int i=0; i < NotConstrainGene.size(); i++)
                     ^
BASiCS_CPPcode.cpp: In function 'Rcpp::List HiddenBASiCS_MCMCcppNoSpikes(int, int, int, Rcpp::NumericMatrix, Rcpp::NumericMatrix, Rcpp::NumericVector, Rcpp::NumericVector, Rcpp::NumericVector, Rcpp::NumericVector, double, double, double, double, double, double, double, double, double, Rcpp::NumericVector, Rcpp::NumericVector, Rcpp::NumericVector, double, Rcpp::NumericVector, Rcpp::NumericVector, int, int, int, double, double, Rcpp::NumericVector, Rcpp::NumericVector, Rcpp::NumericVector, Rcpp::NumericVector, double, Rcpp::NumericVector, int, Rcpp::NumericVector, Rcpp::NumericVector, Rcpp::NumericVector, int)':
BASiCS_CPPcode.cpp:1648:14: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
     if(i%Thin==0 & i>=Burn)
              ^
BASiCS_CPPcode.cpp:1666:19: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
     if(i%(2*Thin) == 0 & PrintProgress == 1)
                   ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/RcppArmadillo/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o BASiCS.dll tmp.def BASiCS_CPPcode.o RcppExports.o -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/x64 -lRlapack -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -LC:/local323/lib/x64 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/BASiCS.buildbin-libdir/BASiCS/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'BASiCS' as BASiCS_1.0.1.zip
* DONE (BASiCS)
In R CMD INSTALL
In R CMD INSTALL

Tests output

BASiCS.Rcheck/tests_i386/testthat.Rout


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

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

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

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, append,
    as.data.frame, cbind, colMeans, colSums, colnames, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
    pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    expand.grid

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")'.

Loading required package: DelayedArray
Loading required package: matrixStats

Attaching package: 'matrixStats'

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

    anyMissing, rowMedians


Attaching package: 'DelayedArray'

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

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

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

    apply

    Welcome to 'BASiCS'. If you used 'BASiCS' before its release in
    Bioconductor, please visit:
    https://github.com/catavallejos/BASiCS/wiki.
> 
> test_check("BASiCS")
-------------------------------------------------------------
MCMC sampler has been started: 1000 iterations to go.
-------------------------------------------------------------
-------------------------------------------------------------
End of Burn-in period.
-------------------------------------------------------------
 
-------------------------------------------------------------
-------------------------------------------------------------
All 1000 MCMC iterations have been completed.
-------------------------------------------------------------
-------------------------------------------------------------
 
-------------------------------------------------------------
Please see below a summary of the overall acceptance rates.
-------------------------------------------------------------
 
Minimum acceptance rate among mu[i]'s: 0.462
Average acceptance rate among mu[i]'s: 0.69876
Maximum acceptance rate among mu[i]'s: 0.856
 
Minimum acceptance rate among delta[i]'s: 0.504
Average acceptance rate among delta[i]'s: 0.58256
Maximum acceptance rate among delta[i]'s: 0.682
 
Acceptance rate for phi (joint): 0.896
 
Minimum acceptance rate among nu[j]'s: 0.468
Average acceptance rate among nu[j]'s: 0.5527
Maximum acceptance rate among nu[j]'s: 0.714
 
Minimum acceptance rate among theta[k]'s: 0.78
Average acceptance rate among theta[k]'s: 0.78
Maximum acceptance rate among theta[k]'s: 0.78
 
-------------------------------------------------------------
 
-------------------------------------------------------------
MCMC sampler has been started: 1000 iterations to go.
-------------------------------------------------------------
-------------------------------------------------------------
End of Burn-in period.
-------------------------------------------------------------
 
-------------------------------------------------------------
-------------------------------------------------------------
All 1000 MCMC iterations have been completed.
-------------------------------------------------------------
-------------------------------------------------------------
 
-------------------------------------------------------------
Please see below a summary of the overall acceptance rates.
-------------------------------------------------------------
 
Minimum acceptance rate among mu[i]'s: 0.514
Average acceptance rate among mu[i]'s: 0.70912
Maximum acceptance rate among mu[i]'s: 0.832
 
Minimum acceptance rate among delta[i]'s: 0.504
Average acceptance rate among delta[i]'s: 0.5884
Maximum acceptance rate among delta[i]'s: 0.736
 
Acceptance rate for phi (joint): 0.898
 
Minimum acceptance rate among nu[j]'s: 0.42
Average acceptance rate among nu[j]'s: 0.5339
Maximum acceptance rate among nu[j]'s: 0.762
 
Minimum acceptance rate among theta[k]'s: 0.828
Average acceptance rate among theta[k]'s: 0.835
Maximum acceptance rate among theta[k]'s: 0.842
 
-------------------------------------------------------------
 
== testthat results  ===========================================================
OK: 39 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  15.51    0.39   15.89 

BASiCS.Rcheck/tests_x64/testthat.Rout


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

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

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

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, append,
    as.data.frame, cbind, colMeans, colSums, colnames, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
    pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    expand.grid

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")'.

Loading required package: DelayedArray
Loading required package: matrixStats

Attaching package: 'matrixStats'

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

    anyMissing, rowMedians


Attaching package: 'DelayedArray'

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

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

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

    apply

    Welcome to 'BASiCS'. If you used 'BASiCS' before its release in
    Bioconductor, please visit:
    https://github.com/catavallejos/BASiCS/wiki.
> 
> test_check("BASiCS")
-------------------------------------------------------------
MCMC sampler has been started: 1000 iterations to go.
-------------------------------------------------------------
-------------------------------------------------------------
End of Burn-in period.
-------------------------------------------------------------
 
-------------------------------------------------------------
-------------------------------------------------------------
All 1000 MCMC iterations have been completed.
-------------------------------------------------------------
-------------------------------------------------------------
 
-------------------------------------------------------------
Please see below a summary of the overall acceptance rates.
-------------------------------------------------------------
 
Minimum acceptance rate among mu[i]'s: 0.462
Average acceptance rate among mu[i]'s: 0.69876
Maximum acceptance rate among mu[i]'s: 0.856
 
Minimum acceptance rate among delta[i]'s: 0.504
Average acceptance rate among delta[i]'s: 0.58256
Maximum acceptance rate among delta[i]'s: 0.682
 
Acceptance rate for phi (joint): 0.896
 
Minimum acceptance rate among nu[j]'s: 0.468
Average acceptance rate among nu[j]'s: 0.5527
Maximum acceptance rate among nu[j]'s: 0.714
 
Minimum acceptance rate among theta[k]'s: 0.78
Average acceptance rate among theta[k]'s: 0.78
Maximum acceptance rate among theta[k]'s: 0.78
 
-------------------------------------------------------------
 
-------------------------------------------------------------
MCMC sampler has been started: 1000 iterations to go.
-------------------------------------------------------------
-------------------------------------------------------------
End of Burn-in period.
-------------------------------------------------------------
 
-------------------------------------------------------------
-------------------------------------------------------------
All 1000 MCMC iterations have been completed.
-------------------------------------------------------------
-------------------------------------------------------------
 
-------------------------------------------------------------
Please see below a summary of the overall acceptance rates.
-------------------------------------------------------------
 
Minimum acceptance rate among mu[i]'s: 0.514
Average acceptance rate among mu[i]'s: 0.70912
Maximum acceptance rate among mu[i]'s: 0.832
 
Minimum acceptance rate among delta[i]'s: 0.504
Average acceptance rate among delta[i]'s: 0.5884
Maximum acceptance rate among delta[i]'s: 0.736
 
Acceptance rate for phi (joint): 0.898
 
Minimum acceptance rate among nu[j]'s: 0.42
Average acceptance rate among nu[j]'s: 0.5339
Maximum acceptance rate among nu[j]'s: 0.762
 
Minimum acceptance rate among theta[k]'s: 0.828
Average acceptance rate among theta[k]'s: 0.835
Maximum acceptance rate among theta[k]'s: 0.842
 
-------------------------------------------------------------
 
== testthat results  ===========================================================
OK: 39 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  13.50    0.25   13.73 

Example timings

BASiCS.Rcheck/examples_i386/BASiCS-Ex.timings

nameusersystemelapsed
BASiCS_Chain-methods0.720.010.94
BASiCS_Chain1.280.031.31
BASiCS_D_TestDE0.190.055.18
BASiCS_DenoisedCounts7.900.027.93
BASiCS_DenoisedRates7.850.007.84
BASiCS_DetectHVG_LVG0.150.000.16
BASiCS_Filter0.030.000.03
BASiCS_LoadChain0.360.000.36
BASiCS_MCMC6.590.147.13
BASiCS_Sim0.050.000.04
BASiCS_Summary-methods0.140.010.16
BASiCS_Summary0.430.000.43
BASiCS_TestDE1.520.031.55
BASiCS_VarThresholdSearchHVG_LVG0.190.000.19
BASiCS_VarianceDecomp0.170.020.19
Summary-BASiCS_Chain-method0.170.000.17
displayChainBASiCS-BASiCS_Chain-method0.140.020.16
displaySummaryBASiCS-BASiCS_Summary-method0.140.030.17
makeExampleBASiCS_Data0.030.000.03
newBASiCS_Chain0.450.000.46
newBASiCS_Data0.070.000.06
plot-BASiCS_Chain-method0.170.000.18
plot-BASiCS_Summary-method0.140.020.15

BASiCS.Rcheck/examples_x64/BASiCS-Ex.timings

nameusersystemelapsed
BASiCS_Chain-methods0.860.000.86
BASiCS_Chain1.360.021.37
BASiCS_D_TestDE0.190.000.18
BASiCS_DenoisedCounts6.920.006.93
BASiCS_DenoisedRates7.470.007.47
BASiCS_DetectHVG_LVG0.220.000.21
BASiCS_Filter0.040.000.05
BASiCS_LoadChain0.600.000.59
BASiCS_MCMC7.840.087.97
BASiCS_Sim0.050.000.05
BASiCS_Summary-methods0.120.030.16
BASiCS_Summary0.580.000.57
BASiCS_TestDE1.560.001.57
BASiCS_VarThresholdSearchHVG_LVG0.160.000.15
BASiCS_VarianceDecomp0.120.030.16
Summary-BASiCS_Chain-method0.110.030.14
displayChainBASiCS-BASiCS_Chain-method0.140.030.17
displaySummaryBASiCS-BASiCS_Summary-method0.160.000.15
makeExampleBASiCS_Data0.040.000.05
newBASiCS_Chain0.660.000.66
newBASiCS_Data0.080.000.08
plot-BASiCS_Chain-method0.130.030.16
plot-BASiCS_Summary-method0.150.000.15