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CHECK report for BASiCS on tokay2

This page was generated on 2018-10-17 08:44:38 -0400 (Wed, 17 Oct 2018).

Package 95/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BASiCS 1.2.1
Catalina A. Vallejos , Nils Eling
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/BASiCS
Branch: RELEASE_3_7
Last Commit: 8351a09
Last Changed Date: 2018-06-05 08:24:54 -0400 (Tue, 05 Jun 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: BASiCS
Version: 1.2.1
Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BASiCS.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings BASiCS_1.2.1.tar.gz
StartedAt: 2018-10-17 00:37:30 -0400 (Wed, 17 Oct 2018)
EndedAt: 2018-10-17 00:43:12 -0400 (Wed, 17 Oct 2018)
EllapsedTime: 342.6 seconds
RetCode: 0
Status:  OK  
CheckDir: BASiCS.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BASiCS.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings BASiCS_1.2.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/BASiCS.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* 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 '1.2.1'
* 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 ... NOTE
  installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   2.4Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking 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-3.7-bioc/R/library/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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
BASiCS_DenoisedCounts 7.94   0.00    7.94
BASiCS_DenoisedRates  7.83   0.00    7.83
BASiCS_MCMC           5.81   0.07    5.89
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
BASiCS_DenoisedRates  7.19   0.00    7.18
BASiCS_DenoisedCounts 7.11   0.00    7.11
BASiCS_MCMC           5.51   0.04    5.56
* 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: 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.7-bioc/meat/BASiCS.Rcheck/00check.log'
for details.

Installation output

BASiCS.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/BASiCS_1.2.1.tar.gz && rm -rf BASiCS.buildbin-libdir && mkdir BASiCS.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=BASiCS.buildbin-libdir BASiCS_1.2.1.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL BASiCS_1.2.1.zip && rm BASiCS_1.2.1.tar.gz BASiCS_1.2.1.zip
###
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100 2301k  100 2301k    0     0  27.6M      0 --:--:-- --:--:-- --:--:-- 29.9M

install for i386

* installing *source* package 'BASiCS' ...
** libs
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/RcppArmadillo/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c BASiCS_DenoisedRates.cpp -o BASiCS_DenoisedRates.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/RcppArmadillo/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c BASiCS_MCMCcpp.cpp -o BASiCS_MCMCcpp.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/RcppArmadillo/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c BASiCS_MCMCcppNoSpikes.cpp -o BASiCS_MCMCcppNoSpikes.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/RcppArmadillo/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c BASiCS_MCMCcppReg.cpp -o BASiCS_MCMCcppReg.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/RcppArmadillo/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c BASiCS_MCMCcppRegNoSpikes.cpp -o BASiCS_MCMCcppRegNoSpikes.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/RcppArmadillo/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/RcppArmadillo/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c general_utils.cpp -o general_utils.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/RcppArmadillo/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c utils_MCMCcpp.cpp -o utils_MCMCcpp.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/RcppArmadillo/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c utils_MCMCcppNoSpikes.cpp -o utils_MCMCcppNoSpikes.o
utils_MCMCcppNoSpikes.cpp: In function 'arma::mat muUpdateNoSpikes(const vec&, const vec&, const mat&, const vec&, const vec&, const vec&, const double&, const int&, const int&, arma::vec&, arma::vec&, arma::vec&, const double&, const int&, const uvec&, const uvec&, const int&)':
utils_MCMCcppNoSpikes.cpp:54:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (int i=0; i < ConstrainGene.size(); i++) {
                   ^
utils_MCMCcppNoSpikes.cpp:75:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int i=0; i < NotConstrainGene.size(); i++) {
                     ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/RcppArmadillo/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c utils_MCMCcppReg.cpp -o utils_MCMCcppReg.o
utils_MCMCcppReg.cpp: In function 'arma::mat designMatrix(const int&, const vec&, const double&)':
utils_MCMCcppReg.cpp:16:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(int i=1; i < myu.size(); i++) {
                  ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/RcppArmadillo/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c utils_MCMCcppRegNoSpikes.cpp -o utils_MCMCcppRegNoSpikes.o
utils_MCMCcppRegNoSpikes.cpp: In function 'arma::mat muUpdateRegNoSpikes(const vec&, const vec&, const mat&, const vec&, const vec&, const vec&, const vec&, const double&, const int&, const int&, arma::vec&, arma::vec&, arma::vec&, const double&, const int&, const uvec&, const uvec&, const int&, const int&, const vec&, const vec&, const mat&, const double&, double)':
utils_MCMCcppRegNoSpikes.cpp:67:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (int i=0; i < ConstrainGene.size(); i++) {
                   ^
utils_MCMCcppRegNoSpikes.cpp:88:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int i=0; i < NotConstrainGene.size(); i++) {
                     ^
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o BASiCS.dll tmp.def BASiCS_DenoisedRates.o BASiCS_MCMCcpp.o BASiCS_MCMCcppNoSpikes.o BASiCS_MCMCcppReg.o BASiCS_MCMCcppRegNoSpikes.o RcppExports.o general_utils.o utils_MCMCcpp.o utils_MCMCcppNoSpikes.o utils_MCMCcppReg.o utils_MCMCcppRegNoSpikes.o -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/i386 -lRlapack -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/i386 -lRblas -lgfortran -lm -lquadmath -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.7-bioc/meat/BASiCS.buildbin-libdir/BASiCS/libs/i386
** R
** data
** inst
** byte-compile and prepare 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  
    BASiCS_showFit-BASiCS_Chain-method      html  
    ChainRNA                                html  
    ChainRNAReg                             html  
    ChainSC                                 html  
    ChainSCReg                              html  
    Summary-BASiCS_Chain-method             html  
    colnames-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  
    rownames-BASiCS_Chain-method            html  
    subset-BASiCS_Chain-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˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/RcppArmadillo/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c BASiCS_DenoisedRates.cpp -o BASiCS_DenoisedRates.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/RcppArmadillo/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c BASiCS_MCMCcpp.cpp -o BASiCS_MCMCcpp.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/RcppArmadillo/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c BASiCS_MCMCcppNoSpikes.cpp -o BASiCS_MCMCcppNoSpikes.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/RcppArmadillo/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c BASiCS_MCMCcppReg.cpp -o BASiCS_MCMCcppReg.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/RcppArmadillo/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c BASiCS_MCMCcppRegNoSpikes.cpp -o BASiCS_MCMCcppRegNoSpikes.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/RcppArmadillo/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/RcppArmadillo/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c general_utils.cpp -o general_utils.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/RcppArmadillo/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c utils_MCMCcpp.cpp -o utils_MCMCcpp.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/RcppArmadillo/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c utils_MCMCcppNoSpikes.cpp -o utils_MCMCcppNoSpikes.o
utils_MCMCcppNoSpikes.cpp: In function 'arma::mat muUpdateNoSpikes(const vec&, const vec&, const mat&, const vec&, const vec&, const vec&, const double&, const int&, const int&, arma::vec&, arma::vec&, arma::vec&, const double&, const int&, const uvec&, const uvec&, const int&)':
utils_MCMCcppNoSpikes.cpp:54:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (int i=0; i < ConstrainGene.size(); i++) {
                   ^
utils_MCMCcppNoSpikes.cpp:75:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int i=0; i < NotConstrainGene.size(); i++) {
                     ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/RcppArmadillo/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c utils_MCMCcppReg.cpp -o utils_MCMCcppReg.o
utils_MCMCcppReg.cpp: In function 'arma::mat designMatrix(const int&, const vec&, const double&)':
utils_MCMCcppReg.cpp:16:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(int i=1; i < myu.size(); i++) {
                  ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/RcppArmadillo/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c utils_MCMCcppRegNoSpikes.cpp -o utils_MCMCcppRegNoSpikes.o
utils_MCMCcppRegNoSpikes.cpp: In function 'arma::mat muUpdateRegNoSpikes(const vec&, const vec&, const mat&, const vec&, const vec&, const vec&, const vec&, const double&, const int&, const int&, arma::vec&, arma::vec&, arma::vec&, const double&, const int&, const uvec&, const uvec&, const int&, const int&, const vec&, const vec&, const mat&, const double&, double)':
utils_MCMCcppRegNoSpikes.cpp:67:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (int i=0; i < ConstrainGene.size(); i++) {
                   ^
utils_MCMCcppRegNoSpikes.cpp:88:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int i=0; i < NotConstrainGene.size(); i++) {
                     ^
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o BASiCS.dll tmp.def BASiCS_DenoisedRates.o BASiCS_MCMCcpp.o BASiCS_MCMCcppNoSpikes.o BASiCS_MCMCcppReg.o BASiCS_MCMCcppRegNoSpikes.o RcppExports.o general_utils.o utils_MCMCcpp.o utils_MCMCcppNoSpikes.o utils_MCMCcppReg.o utils_MCMCcppRegNoSpikes.o -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/x64 -lRlapack -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.7-bioc/meat/BASiCS.buildbin-libdir/BASiCS/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'BASiCS' as BASiCS_1.2.1.zip
* DONE (BASiCS)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'BASiCS' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output

BASiCS.Rcheck/tests_i386/testthat.Rout


R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
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, basename, cbind, colMeans, colSums, colnames,
    dirname, 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

Attaching package: 'IRanges'

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

    windows

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

Loading required package: BiocParallel

Attaching package: 'DelayedArray'

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

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

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

    aperm, 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: 0.5
Average acceptance rate among mu[i]'s: 0.70156
Maximum acceptance rate among mu[i]'s: 0.818
 
 
Minimum acceptance rate among delta[i]'s: 0.508
Average acceptance rate among delta[i]'s: 0.58948
Maximum acceptance rate among delta[i]'s: 0.726
 
 
Acceptance rate for phi (joint): 0.89
 
 
Minimum acceptance rate among nu[j]'s: 0.428
Average acceptance rate among nu[j]'s: 0.5352
Maximum acceptance rate among nu[j]'s: 0.728
 
 
Minimum acceptance rate among theta[k]'s: 0.762
Average acceptance rate among theta[k]'s: 0.762
Maximum acceptance rate among theta[k]'s: 0.762
 
-----------------------------------------------------
 
-----------------------------------------------------
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: 0.524
Average acceptance rate among mu[i]'s: 0.70608
Maximum acceptance rate among mu[i]'s: 0.846
 
 
Minimum acceptance rate among delta[i]'s: 0.492
Average acceptance rate among delta[i]'s: 0.58968
Maximum acceptance rate among delta[i]'s: 0.708
 
 
Acceptance rate for phi (joint): 0.912
 
 
Minimum acceptance rate among nu[j]'s: 0.438
Average acceptance rate among nu[j]'s: 0.545
Maximum acceptance rate among nu[j]'s: 0.698
 
 
Minimum acceptance rate among theta[k]'s: 0.832
Average acceptance rate among theta[k]'s: 0.833
Maximum acceptance rate among theta[k]'s: 0.834
 
-----------------------------------------------------
 
-----------------------------------------------------
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: 0.502
Average acceptance rate among mu[i]'s: 0.67984
Maximum acceptance rate among mu[i]'s: 0.834
 
 
Minimum acceptance rate among delta[i]'s: 0.452
Average acceptance rate among delta[i]'s: 0.53276
Maximum acceptance rate among delta[i]'s: 0.642
 
 
Minimum acceptance rate among nu[jk]'s: 0.83
Average acceptance rate among nu[jk]'s: 0.919
Maximum acceptance rate among nu[jk]'s: 0.978
 
 
Minimum acceptance rate among theta[k]'s: 0.834
Average acceptance rate among theta[k]'s: 0.844
Maximum acceptance rate among theta[k]'s: 0.854
 
-----------------------------------------------------
 
-----------------------------------------------------
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: 0.528
Average acceptance rate among mu[i]'s: 0.7122
Maximum acceptance rate among mu[i]'s: 0.832
 
 
Minimum acceptance rate among delta[i]'s: 0.524
Average acceptance rate among delta[i]'s: 0.5806
Maximum acceptance rate among delta[i]'s: 0.672
 
 
Minimum acceptance rate among nu[jk]'s: 0.814
Average acceptance rate among nu[jk]'s: 0.9311
Maximum acceptance rate among nu[jk]'s: 0.982
 
 
Minimum acceptance rate among theta[k]'s: 0.83
Average acceptance rate among theta[k]'s: 0.838
Maximum acceptance rate among theta[k]'s: 0.846
 
-----------------------------------------------------
 
-----------------------------------------------------
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: 0.528
Average acceptance rate among mu[i]'s: 0.7122
Maximum acceptance rate among mu[i]'s: 0.832
 
 
Minimum acceptance rate among delta[i]'s: 0.524
Average acceptance rate among delta[i]'s: 0.5806
Maximum acceptance rate among delta[i]'s: 0.672
 
 
Minimum acceptance rate among nu[jk]'s: 0.814
Average acceptance rate among nu[jk]'s: 0.9311
Maximum acceptance rate among nu[jk]'s: 0.982
 
 
Minimum acceptance rate among theta[k]'s: 0.83
Average acceptance rate among theta[k]'s: 0.838
Maximum acceptance rate among theta[k]'s: 0.846
 
-----------------------------------------------------
 
-----------------------------------------------------
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: 0.454
Average acceptance rate among mu[i]'s: 0.63564
Maximum acceptance rate among mu[i]'s: 0.85
 
 
Minimum acceptance rate among delta[i]'s: 0.476
Average acceptance rate among delta[i]'s: 0.5298
Maximum acceptance rate among delta[i]'s: 0.602
 
 
Minimum acceptance rate among nu[jk]'s: 0.79
Average acceptance rate among nu[jk]'s: 0.91
Maximum acceptance rate among nu[jk]'s: 0.978
 
 
Minimum acceptance rate among theta[k]'s: 0.828
Average acceptance rate among theta[k]'s: 0.834
Maximum acceptance rate among theta[k]'s: 0.84
 
 
-----------------------------------------------------
 
-----------------------------------------------------
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: 0.64652
Maximum acceptance rate among mu[i]'s: 0.848
 
 
Minimum acceptance rate among delta[i]'s: 0.444
Average acceptance rate among delta[i]'s: 0.5508
Maximum acceptance rate among delta[i]'s: 0.64
 
 
Acceptance rate for phi (joint): 0.89
 
 
Minimum acceptance rate among nu[j]'s: 0.39
Average acceptance rate among nu[j]'s: 0.5373
Maximum acceptance rate among nu[j]'s: 0.716
 
 
Minimum acceptance rate among theta[k]'s: 0.834
Average acceptance rate among theta[k]'s: 0.843
Maximum acceptance rate among theta[k]'s: 0.852
 
-----------------------------------------------------
 
== testthat results  ===========================================================
OK: 112 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  20.51    1.04   21.53

BASiCS.Rcheck/tests_x64/testthat.Rout


R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
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, basename, cbind, colMeans, colSums, colnames,
    dirname, 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

Attaching package: 'IRanges'

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

    windows

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

Loading required package: BiocParallel

Attaching package: 'DelayedArray'

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

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

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

    aperm, 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: 0.5
Average acceptance rate among mu[i]'s: 0.70156
Maximum acceptance rate among mu[i]'s: 0.818
 
 
Minimum acceptance rate among delta[i]'s: 0.508
Average acceptance rate among delta[i]'s: 0.58948
Maximum acceptance rate among delta[i]'s: 0.726
 
 
Acceptance rate for phi (joint): 0.89
 
 
Minimum acceptance rate among nu[j]'s: 0.428
Average acceptance rate among nu[j]'s: 0.5352
Maximum acceptance rate among nu[j]'s: 0.728
 
 
Minimum acceptance rate among theta[k]'s: 0.762
Average acceptance rate among theta[k]'s: 0.762
Maximum acceptance rate among theta[k]'s: 0.762
 
-----------------------------------------------------
 
-----------------------------------------------------
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: 0.524
Average acceptance rate among mu[i]'s: 0.70608
Maximum acceptance rate among mu[i]'s: 0.846
 
 
Minimum acceptance rate among delta[i]'s: 0.492
Average acceptance rate among delta[i]'s: 0.58968
Maximum acceptance rate among delta[i]'s: 0.708
 
 
Acceptance rate for phi (joint): 0.912
 
 
Minimum acceptance rate among nu[j]'s: 0.438
Average acceptance rate among nu[j]'s: 0.545
Maximum acceptance rate among nu[j]'s: 0.698
 
 
Minimum acceptance rate among theta[k]'s: 0.832
Average acceptance rate among theta[k]'s: 0.833
Maximum acceptance rate among theta[k]'s: 0.834
 
-----------------------------------------------------
 
-----------------------------------------------------
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: 0.502
Average acceptance rate among mu[i]'s: 0.67984
Maximum acceptance rate among mu[i]'s: 0.834
 
 
Minimum acceptance rate among delta[i]'s: 0.452
Average acceptance rate among delta[i]'s: 0.53276
Maximum acceptance rate among delta[i]'s: 0.642
 
 
Minimum acceptance rate among nu[jk]'s: 0.83
Average acceptance rate among nu[jk]'s: 0.919
Maximum acceptance rate among nu[jk]'s: 0.978
 
 
Minimum acceptance rate among theta[k]'s: 0.834
Average acceptance rate among theta[k]'s: 0.844
Maximum acceptance rate among theta[k]'s: 0.854
 
-----------------------------------------------------
 
-----------------------------------------------------
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: 0.528
Average acceptance rate among mu[i]'s: 0.7122
Maximum acceptance rate among mu[i]'s: 0.832
 
 
Minimum acceptance rate among delta[i]'s: 0.524
Average acceptance rate among delta[i]'s: 0.5806
Maximum acceptance rate among delta[i]'s: 0.672
 
 
Minimum acceptance rate among nu[jk]'s: 0.814
Average acceptance rate among nu[jk]'s: 0.9311
Maximum acceptance rate among nu[jk]'s: 0.982
 
 
Minimum acceptance rate among theta[k]'s: 0.83
Average acceptance rate among theta[k]'s: 0.838
Maximum acceptance rate among theta[k]'s: 0.846
 
-----------------------------------------------------
 
-----------------------------------------------------
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: 0.528
Average acceptance rate among mu[i]'s: 0.7122
Maximum acceptance rate among mu[i]'s: 0.832
 
 
Minimum acceptance rate among delta[i]'s: 0.524
Average acceptance rate among delta[i]'s: 0.5806
Maximum acceptance rate among delta[i]'s: 0.672
 
 
Minimum acceptance rate among nu[jk]'s: 0.814
Average acceptance rate among nu[jk]'s: 0.9311
Maximum acceptance rate among nu[jk]'s: 0.982
 
 
Minimum acceptance rate among theta[k]'s: 0.83
Average acceptance rate among theta[k]'s: 0.838
Maximum acceptance rate among theta[k]'s: 0.846
 
-----------------------------------------------------
 
-----------------------------------------------------
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: 0.454
Average acceptance rate among mu[i]'s: 0.63564
Maximum acceptance rate among mu[i]'s: 0.85
 
 
Minimum acceptance rate among delta[i]'s: 0.476
Average acceptance rate among delta[i]'s: 0.5298
Maximum acceptance rate among delta[i]'s: 0.602
 
 
Minimum acceptance rate among nu[jk]'s: 0.79
Average acceptance rate among nu[jk]'s: 0.91
Maximum acceptance rate among nu[jk]'s: 0.978
 
 
Minimum acceptance rate among theta[k]'s: 0.828
Average acceptance rate among theta[k]'s: 0.834
Maximum acceptance rate among theta[k]'s: 0.84
 
 
-----------------------------------------------------
 
-----------------------------------------------------
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: 0.64652
Maximum acceptance rate among mu[i]'s: 0.848
 
 
Minimum acceptance rate among delta[i]'s: 0.444
Average acceptance rate among delta[i]'s: 0.5508
Maximum acceptance rate among delta[i]'s: 0.64
 
 
Acceptance rate for phi (joint): 0.89
 
 
Minimum acceptance rate among nu[j]'s: 0.39
Average acceptance rate among nu[j]'s: 0.5373
Maximum acceptance rate among nu[j]'s: 0.716
 
 
Minimum acceptance rate among theta[k]'s: 0.834
Average acceptance rate among theta[k]'s: 0.843
Maximum acceptance rate among theta[k]'s: 0.852
 
-----------------------------------------------------
 
== testthat results  ===========================================================
OK: 112 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  20.64    0.51   21.14

Example timings

BASiCS.Rcheck/examples_i386/BASiCS-Ex.timings

nameusersystemelapsed
BASiCS_Chain-methods0.780.000.81
BASiCS_Chain1.270.001.34
BASiCS_D_TestDE0.350.040.53
BASiCS_DenoisedCounts7.940.007.94
BASiCS_DenoisedRates7.830.007.83
BASiCS_DetectHVG_LVG0.150.000.19
BASiCS_Filter0.050.010.06
BASiCS_LoadChain0.640.020.66
BASiCS_MCMC5.810.075.89
BASiCS_Sim0.060.000.06
BASiCS_Summary-methods0.200.020.21
BASiCS_Summary0.780.000.79
BASiCS_TestDE2.790.092.87
BASiCS_VarThresholdSearchHVG_LVG0.140.040.17
BASiCS_VarianceDecomp0.060.030.10
BASiCS_showFit-BASiCS_Chain-method0.490.010.50
Summary-BASiCS_Chain-method0.150.020.15
colnames-BASiCS_Chain-method0.100.040.16
displayChainBASiCS-BASiCS_Chain-method0.150.020.16
displaySummaryBASiCS-BASiCS_Summary-method0.150.000.15
makeExampleBASiCS_Data0.060.000.06
newBASiCS_Chain1.10.01.1
newBASiCS_Data0.150.000.15
plot-BASiCS_Chain-method0.140.020.16
plot-BASiCS_Summary-method0.140.010.15
rownames-BASiCS_Chain-method0.140.020.16
subset-BASiCS_Chain-method0.130.030.16

BASiCS.Rcheck/examples_x64/BASiCS-Ex.timings

nameusersystemelapsed
BASiCS_Chain-methods1.090.001.10
BASiCS_Chain1.780.001.78
BASiCS_D_TestDE0.260.000.27
BASiCS_DenoisedCounts7.110.007.11
BASiCS_DenoisedRates7.190.007.18
BASiCS_DetectHVG_LVG0.140.040.18
BASiCS_Filter0.060.000.06
BASiCS_LoadChain0.660.000.66
BASiCS_MCMC5.510.045.56
BASiCS_Sim0.060.000.06
BASiCS_Summary-methods0.120.030.16
BASiCS_Summary0.750.000.75
BASiCS_TestDE2.490.082.56
BASiCS_VarThresholdSearchHVG_LVG0.140.020.16
BASiCS_VarianceDecomp0.090.010.11
BASiCS_showFit-BASiCS_Chain-method0.570.000.56
Summary-BASiCS_Chain-method0.140.010.16
colnames-BASiCS_Chain-method0.110.030.14
displayChainBASiCS-BASiCS_Chain-method0.130.020.14
displaySummaryBASiCS-BASiCS_Summary-method0.160.000.15
makeExampleBASiCS_Data0.060.000.07
newBASiCS_Chain1.470.001.47
newBASiCS_Data0.20.00.2
plot-BASiCS_Chain-method0.160.000.16
plot-BASiCS_Summary-method0.140.010.15
rownames-BASiCS_Chain-method0.140.020.16
subset-BASiCS_Chain-method0.130.050.17