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CHECK report for BASiCS on malbec2

This page was generated on 2018-10-17 08:30:45 -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: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:BASiCS.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings BASiCS_1.2.1.tar.gz
StartedAt: 2018-10-15 22:38:04 -0400 (Mon, 15 Oct 2018)
EndedAt: 2018-10-15 22:41:01 -0400 (Mon, 15 Oct 2018)
EllapsedTime: 176.4 seconds
RetCode: 0
Status:  OK 
CheckDir: BASiCS.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:BASiCS.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings BASiCS_1.2.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/BASiCS.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘BASiCS’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 12.9Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs  10.3Mb
* 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 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 is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
BASiCS_DenoisedRates  5.872  0.000   5.876
BASiCS_DenoisedCounts 5.644  0.084   5.734
* 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 ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.7-bioc/meat/BASiCS.Rcheck/00check.log’
for details.

Installation output

BASiCS.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL BASiCS
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/library’
* installing *source* package ‘BASiCS’ ...
** libs
g++  -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/RcppArmadillo/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c BASiCS_DenoisedRates.cpp -o BASiCS_DenoisedRates.o
In file included from /home/biocbuild/bbs-3.7-bioc/R/library/RcppArmadillo/include/armadillo:54:0,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/RcppArmadillo/include/RcppArmadilloForward.h:46,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/RcppArmadillo/include/RcppArmadillo.h:31,
                 from MCMCcpp.h:15,
                 from utils.h:1,
                 from BASiCS_DenoisedRates.cpp:1:
/home/biocbuild/bbs-3.7-bioc/R/library/RcppArmadillo/include/armadillo_bits/compiler_setup.hpp:509:108: note: #pragma message: NOTE: suggest to enable C++14 mode for faster code; add -std=c++14 to compiler flags
     #pragma message ("NOTE: suggest to enable C++14 mode for faster code; add -std=c++14 to compiler flags")
                                                                                                            ^
g++  -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/RcppArmadillo/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c BASiCS_MCMCcpp.cpp -o BASiCS_MCMCcpp.o
In file included from /home/biocbuild/bbs-3.7-bioc/R/library/RcppArmadillo/include/armadillo:54:0,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/RcppArmadillo/include/RcppArmadilloForward.h:46,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/RcppArmadillo/include/RcppArmadillo.h:31,
                 from MCMCcpp.h:15,
                 from utils.h:1,
                 from BASiCS_MCMCcpp.cpp:1:
/home/biocbuild/bbs-3.7-bioc/R/library/RcppArmadillo/include/armadillo_bits/compiler_setup.hpp:509:108: note: #pragma message: NOTE: suggest to enable C++14 mode for faster code; add -std=c++14 to compiler flags
     #pragma message ("NOTE: suggest to enable C++14 mode for faster code; add -std=c++14 to compiler flags")
                                                                                                            ^
g++  -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/RcppArmadillo/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c BASiCS_MCMCcppNoSpikes.cpp -o BASiCS_MCMCcppNoSpikes.o
In file included from /home/biocbuild/bbs-3.7-bioc/R/library/RcppArmadillo/include/armadillo:54:0,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/RcppArmadillo/include/RcppArmadilloForward.h:46,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/RcppArmadillo/include/RcppArmadillo.h:31,
                 from MCMCcpp.h:15,
                 from utils.h:1,
                 from BASiCS_MCMCcppNoSpikes.cpp:1:
/home/biocbuild/bbs-3.7-bioc/R/library/RcppArmadillo/include/armadillo_bits/compiler_setup.hpp:509:108: note: #pragma message: NOTE: suggest to enable C++14 mode for faster code; add -std=c++14 to compiler flags
     #pragma message ("NOTE: suggest to enable C++14 mode for faster code; add -std=c++14 to compiler flags")
                                                                                                            ^
g++  -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/RcppArmadillo/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c BASiCS_MCMCcppReg.cpp -o BASiCS_MCMCcppReg.o
In file included from /home/biocbuild/bbs-3.7-bioc/R/library/RcppArmadillo/include/armadillo:54:0,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/RcppArmadillo/include/RcppArmadilloForward.h:46,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/RcppArmadillo/include/RcppArmadillo.h:31,
                 from MCMCcpp.h:15,
                 from utils.h:1,
                 from BASiCS_MCMCcppReg.cpp:1:
/home/biocbuild/bbs-3.7-bioc/R/library/RcppArmadillo/include/armadillo_bits/compiler_setup.hpp:509:108: note: #pragma message: NOTE: suggest to enable C++14 mode for faster code; add -std=c++14 to compiler flags
     #pragma message ("NOTE: suggest to enable C++14 mode for faster code; add -std=c++14 to compiler flags")
                                                                                                            ^
g++  -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/RcppArmadillo/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c BASiCS_MCMCcppRegNoSpikes.cpp -o BASiCS_MCMCcppRegNoSpikes.o
In file included from /home/biocbuild/bbs-3.7-bioc/R/library/RcppArmadillo/include/armadillo:54:0,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/RcppArmadillo/include/RcppArmadilloForward.h:46,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/RcppArmadillo/include/RcppArmadillo.h:31,
                 from MCMCcpp.h:15,
                 from utils.h:1,
                 from BASiCS_MCMCcppRegNoSpikes.cpp:1:
/home/biocbuild/bbs-3.7-bioc/R/library/RcppArmadillo/include/armadillo_bits/compiler_setup.hpp:509:108: note: #pragma message: NOTE: suggest to enable C++14 mode for faster code; add -std=c++14 to compiler flags
     #pragma message ("NOTE: suggest to enable C++14 mode for faster code; add -std=c++14 to compiler flags")
                                                                                                            ^
g++  -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/RcppArmadillo/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
In file included from /home/biocbuild/bbs-3.7-bioc/R/library/RcppArmadillo/include/armadillo:54:0,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/RcppArmadillo/include/RcppArmadilloForward.h:46,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/RcppArmadillo/include/RcppArmadillo.h:31,
                 from RcppExports.cpp:4:
/home/biocbuild/bbs-3.7-bioc/R/library/RcppArmadillo/include/armadillo_bits/compiler_setup.hpp:509:108: note: #pragma message: NOTE: suggest to enable C++14 mode for faster code; add -std=c++14 to compiler flags
     #pragma message ("NOTE: suggest to enable C++14 mode for faster code; add -std=c++14 to compiler flags")
                                                                                                            ^
g++  -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/RcppArmadillo/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c general_utils.cpp -o general_utils.o
In file included from /home/biocbuild/bbs-3.7-bioc/R/library/RcppArmadillo/include/armadillo:54:0,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/RcppArmadillo/include/RcppArmadilloForward.h:46,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/RcppArmadillo/include/RcppArmadillo.h:31,
                 from MCMCcpp.h:15,
                 from utils.h:1,
                 from general_utils.cpp:1:
/home/biocbuild/bbs-3.7-bioc/R/library/RcppArmadillo/include/armadillo_bits/compiler_setup.hpp:509:108: note: #pragma message: NOTE: suggest to enable C++14 mode for faster code; add -std=c++14 to compiler flags
     #pragma message ("NOTE: suggest to enable C++14 mode for faster code; add -std=c++14 to compiler flags")
                                                                                                            ^
g++  -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/RcppArmadillo/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c utils_MCMCcpp.cpp -o utils_MCMCcpp.o
In file included from /home/biocbuild/bbs-3.7-bioc/R/library/RcppArmadillo/include/armadillo:54:0,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/RcppArmadillo/include/RcppArmadilloForward.h:46,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/RcppArmadillo/include/RcppArmadillo.h:31,
                 from MCMCcpp.h:15,
                 from utils.h:1,
                 from utils_MCMCcpp.cpp:1:
/home/biocbuild/bbs-3.7-bioc/R/library/RcppArmadillo/include/armadillo_bits/compiler_setup.hpp:509:108: note: #pragma message: NOTE: suggest to enable C++14 mode for faster code; add -std=c++14 to compiler flags
     #pragma message ("NOTE: suggest to enable C++14 mode for faster code; add -std=c++14 to compiler flags")
                                                                                                            ^
g++  -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/RcppArmadillo/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c utils_MCMCcppNoSpikes.cpp -o utils_MCMCcppNoSpikes.o
In file included from /home/biocbuild/bbs-3.7-bioc/R/library/RcppArmadillo/include/armadillo:54:0,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/RcppArmadillo/include/RcppArmadilloForward.h:46,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/RcppArmadillo/include/RcppArmadillo.h:31,
                 from MCMCcpp.h:15,
                 from utils.h:1,
                 from utils_MCMCcppNoSpikes.cpp:1:
/home/biocbuild/bbs-3.7-bioc/R/library/RcppArmadillo/include/armadillo_bits/compiler_setup.hpp:509:108: note: #pragma message: NOTE: suggest to enable C++14 mode for faster code; add -std=c++14 to compiler flags
     #pragma message ("NOTE: suggest to enable C++14 mode for faster code; add -std=c++14 to compiler flags")
                                                                                                            ^
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++) {
                     ^
g++  -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/RcppArmadillo/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c utils_MCMCcppReg.cpp -o utils_MCMCcppReg.o
In file included from /home/biocbuild/bbs-3.7-bioc/R/library/RcppArmadillo/include/armadillo:54:0,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/RcppArmadillo/include/RcppArmadilloForward.h:46,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/RcppArmadillo/include/RcppArmadillo.h:31,
                 from MCMCcpp.h:15,
                 from utils.h:1,
                 from utils_MCMCcppReg.cpp:1:
/home/biocbuild/bbs-3.7-bioc/R/library/RcppArmadillo/include/armadillo_bits/compiler_setup.hpp:509:108: note: #pragma message: NOTE: suggest to enable C++14 mode for faster code; add -std=c++14 to compiler flags
     #pragma message ("NOTE: suggest to enable C++14 mode for faster code; add -std=c++14 to compiler flags")
                                                                                                            ^
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++) {
                  ^
g++  -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/RcppArmadillo/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c utils_MCMCcppRegNoSpikes.cpp -o utils_MCMCcppRegNoSpikes.o
In file included from /home/biocbuild/bbs-3.7-bioc/R/library/RcppArmadillo/include/armadillo:54:0,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/RcppArmadillo/include/RcppArmadilloForward.h:46,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/RcppArmadillo/include/RcppArmadillo.h:31,
                 from MCMCcpp.h:15,
                 from utils.h:1,
                 from utils_MCMCcppRegNoSpikes.cpp:1:
/home/biocbuild/bbs-3.7-bioc/R/library/RcppArmadillo/include/armadillo_bits/compiler_setup.hpp:509:108: note: #pragma message: NOTE: suggest to enable C++14 mode for faster code; add -std=c++14 to compiler flags
     #pragma message ("NOTE: suggest to enable C++14 mode for faster code; add -std=c++14 to compiler flags")
                                                                                                            ^
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++) {
                     ^
g++ -shared -L/home/biocbuild/bbs-3.7-bioc/R/lib -L/usr/local/lib -o BASiCS.so 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 -L/home/biocbuild/bbs-3.7-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-3.7-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.7-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.7-bioc/R/library/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
* DONE (BASiCS)

Tests output

BASiCS.Rcheck/tests/testthat.Rout


R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-pc-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: 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
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 
 15.972   0.296  16.282

Example timings

BASiCS.Rcheck/BASiCS-Ex.timings

nameusersystemelapsed
BASiCS_Chain-methods1.1760.0001.183
BASiCS_Chain1.2280.0041.231
BASiCS_D_TestDE0.1880.0440.501
BASiCS_DenoisedCounts5.6440.0845.734
BASiCS_DenoisedRates5.8720.0005.876
BASiCS_DetectHVG_LVG0.1040.0200.130
BASiCS_Filter0.0680.0080.080
BASiCS_LoadChain0.6480.1080.760
BASiCS_MCMC3.9680.1404.122
BASiCS_Sim0.0640.0120.077
BASiCS_Summary-methods0.1080.0280.137
BASiCS_Summary0.6840.0800.764
BASiCS_TestDE1.9440.0081.953
BASiCS_VarThresholdSearchHVG_LVG0.1360.0360.182
BASiCS_VarianceDecomp0.0840.0000.086
BASiCS_showFit-BASiCS_Chain-method0.4920.0560.547
Summary-BASiCS_Chain-method0.1000.0320.178
colnames-BASiCS_Chain-method0.1040.0320.142
displayChainBASiCS-BASiCS_Chain-method0.1200.0360.164
displaySummaryBASiCS-BASiCS_Summary-method0.1160.0320.152
makeExampleBASiCS_Data0.0680.0000.071
newBASiCS_Chain1.2040.0961.304
newBASiCS_Data0.1760.0000.177
plot-BASiCS_Chain-method0.0960.0320.130
plot-BASiCS_Summary-method0.1320.0400.182
rownames-BASiCS_Chain-method0.1360.0520.194
subset-BASiCS_Chain-method0.1080.0360.144