Catalina A. Vallejos
| 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) |
| Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 08:58:53 -0400 (Wed, 17 Oct 2018).
| Package 95/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| BASiCS 1.2.1 Catalina A. Vallejos
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: BASiCS |
| Version: 1.2.1 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:BASiCS.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings BASiCS_1.2.1.tar.gz |
| StartedAt: 2018-10-16 19:59:55 -0400 (Tue, 16 Oct 2018) |
| EndedAt: 2018-10-16 20:04:02 -0400 (Tue, 16 Oct 2018) |
| EllapsedTime: 247.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BASiCS.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:BASiCS.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings BASiCS_1.2.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/BASiCS.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-apple-darwin15.6.0 (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 ... 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
* 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_MCMC 7.116 0.285 7.461
BASiCS_DenoisedRates 5.813 0.017 5.888
BASiCS_DenoisedCounts 5.742 0.013 5.818
* 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: 1 NOTE
See
‘/Users/biocbuild/bbs-3.7-bioc/meat/BASiCS.Rcheck/00check.log’
for details.
BASiCS.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL BASiCS
###
##############################################################################
##############################################################################
* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘BASiCS’ ...
** libs
clang++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppArmadillo/include" -I/usr/local/include -fPIC -Wall -g -O2 -c BASiCS_DenoisedRates.cpp -o BASiCS_DenoisedRates.o
In file included from BASiCS_DenoisedRates.cpp:1:
In file included from ./utils.h:1:
In file included from ./MCMCcpp.h:15:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppArmadillo/include/RcppArmadillo.h:31:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppArmadillo/include/RcppArmadilloForward.h:26:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include/RcppCommon.h:128:
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include/Rcpp/exceptions.h:109:53: warning: all paths through this function will call itself [-Winfinite-recursion]
inline void warning(const std::string& message) { // #nocov start
^
1 warning generated.
clang++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppArmadillo/include" -I/usr/local/include -fPIC -Wall -g -O2 -c BASiCS_MCMCcpp.cpp -o BASiCS_MCMCcpp.o
In file included from BASiCS_MCMCcpp.cpp:1:
In file included from ./utils.h:1:
In file included from ./MCMCcpp.h:15:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppArmadillo/include/RcppArmadillo.h:31:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppArmadillo/include/RcppArmadilloForward.h:26:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include/RcppCommon.h:128:
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include/Rcpp/exceptions.h:109:53: warning: all paths through this function will call itself [-Winfinite-recursion]
inline void warning(const std::string& message) { // #nocov start
^
1 warning generated.
clang++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppArmadillo/include" -I/usr/local/include -fPIC -Wall -g -O2 -c BASiCS_MCMCcppNoSpikes.cpp -o BASiCS_MCMCcppNoSpikes.o
In file included from BASiCS_MCMCcppNoSpikes.cpp:1:
In file included from ./utils.h:1:
In file included from ./MCMCcpp.h:15:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppArmadillo/include/RcppArmadillo.h:31:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppArmadillo/include/RcppArmadilloForward.h:26:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include/RcppCommon.h:128:
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include/Rcpp/exceptions.h:109:53: warning: all paths through this function will call itself [-Winfinite-recursion]
inline void warning(const std::string& message) { // #nocov start
^
1 warning generated.
clang++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppArmadillo/include" -I/usr/local/include -fPIC -Wall -g -O2 -c BASiCS_MCMCcppReg.cpp -o BASiCS_MCMCcppReg.o
In file included from BASiCS_MCMCcppReg.cpp:1:
In file included from ./utils.h:1:
In file included from ./MCMCcpp.h:15:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppArmadillo/include/RcppArmadillo.h:31:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppArmadillo/include/RcppArmadilloForward.h:26:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include/RcppCommon.h:128:
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include/Rcpp/exceptions.h:109:53: warning: all paths through this function will call itself [-Winfinite-recursion]
inline void warning(const std::string& message) { // #nocov start
^
1 warning generated.
clang++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppArmadillo/include" -I/usr/local/include -fPIC -Wall -g -O2 -c BASiCS_MCMCcppRegNoSpikes.cpp -o BASiCS_MCMCcppRegNoSpikes.o
In file included from BASiCS_MCMCcppRegNoSpikes.cpp:1:
In file included from ./utils.h:1:
In file included from ./MCMCcpp.h:15:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppArmadillo/include/RcppArmadillo.h:31:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppArmadillo/include/RcppArmadilloForward.h:26:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include/RcppCommon.h:128:
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include/Rcpp/exceptions.h:109:53: warning: all paths through this function will call itself [-Winfinite-recursion]
inline void warning(const std::string& message) { // #nocov start
^
1 warning generated.
clang++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppArmadillo/include" -I/usr/local/include -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
clang++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppArmadillo/include" -I/usr/local/include -fPIC -Wall -g -O2 -c general_utils.cpp -o general_utils.o
In file included from general_utils.cpp:1:
In file included from ./utils.h:1:
In file included from ./MCMCcpp.h:15:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppArmadillo/include/RcppArmadillo.h:31:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppArmadillo/include/RcppArmadilloForward.h:26:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include/RcppCommon.h:128:
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include/Rcpp/exceptions.h:109:53: warning: all paths through this function will call itself [-Winfinite-recursion]
inline void warning(const std::string& message) { // #nocov start
^
1 warning generated.
clang++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppArmadillo/include" -I/usr/local/include -fPIC -Wall -g -O2 -c utils_MCMCcpp.cpp -o utils_MCMCcpp.o
In file included from utils_MCMCcpp.cpp:1:
In file included from ./utils.h:1:
In file included from ./MCMCcpp.h:15:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppArmadillo/include/RcppArmadillo.h:31:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppArmadillo/include/RcppArmadilloForward.h:26:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include/RcppCommon.h:128:
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include/Rcpp/exceptions.h:109:53: warning: all paths through this function will call itself [-Winfinite-recursion]
inline void warning(const std::string& message) { // #nocov start
^
1 warning generated.
clang++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppArmadillo/include" -I/usr/local/include -fPIC -Wall -g -O2 -c utils_MCMCcppNoSpikes.cpp -o utils_MCMCcppNoSpikes.o
In file included from utils_MCMCcppNoSpikes.cpp:1:
In file included from ./utils.h:1:
In file included from ./MCMCcpp.h:15:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppArmadillo/include/RcppArmadillo.h:31:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppArmadillo/include/RcppArmadilloForward.h:26:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include/RcppCommon.h:128:
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include/Rcpp/exceptions.h:109:53: warning: all paths through this function will call itself [-Winfinite-recursion]
inline void warning(const std::string& message) { // #nocov start
^
1 warning generated.
clang++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppArmadillo/include" -I/usr/local/include -fPIC -Wall -g -O2 -c utils_MCMCcppReg.cpp -o utils_MCMCcppReg.o
In file included from utils_MCMCcppReg.cpp:1:
In file included from ./utils.h:1:
In file included from ./MCMCcpp.h:15:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppArmadillo/include/RcppArmadillo.h:31:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppArmadillo/include/RcppArmadilloForward.h:26:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include/RcppCommon.h:128:
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include/Rcpp/exceptions.h:109:53: warning: all paths through this function will call itself [-Winfinite-recursion]
inline void warning(const std::string& message) { // #nocov start
^
1 warning generated.
clang++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppArmadillo/include" -I/usr/local/include -fPIC -Wall -g -O2 -c utils_MCMCcppRegNoSpikes.cpp -o utils_MCMCcppRegNoSpikes.o
In file included from utils_MCMCcppRegNoSpikes.cpp:1:
In file included from ./utils.h:1:
In file included from ./MCMCcpp.h:15:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppArmadillo/include/RcppArmadillo.h:31:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppArmadillo/include/RcppArmadilloForward.h:26:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include/RcppCommon.h:128:
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include/Rcpp/exceptions.h:109:53: warning: all paths through this function will call itself [-Winfinite-recursion]
inline void warning(const std::string& message) { // #nocov start
^
1 warning generated.
clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/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/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.5/Resources/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)
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-apple-darwin15.6.0 (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
21.000 0.689 21.848
BASiCS.Rcheck/BASiCS-Ex.timings
| name | user | system | elapsed | |
| BASiCS_Chain-methods | 1.047 | 0.008 | 1.066 | |
| BASiCS_Chain | 1.455 | 0.015 | 1.483 | |
| BASiCS_D_TestDE | 0.225 | 0.029 | 0.266 | |
| BASiCS_DenoisedCounts | 5.742 | 0.013 | 5.818 | |
| BASiCS_DenoisedRates | 5.813 | 0.017 | 5.888 | |
| BASiCS_DetectHVG_LVG | 0.180 | 0.020 | 0.202 | |
| BASiCS_Filter | 0.069 | 0.000 | 0.069 | |
| BASiCS_LoadChain | 0.681 | 0.006 | 0.691 | |
| BASiCS_MCMC | 7.116 | 0.285 | 7.461 | |
| BASiCS_Sim | 0.076 | 0.000 | 0.076 | |
| BASiCS_Summary-methods | 0.173 | 0.018 | 0.192 | |
| BASiCS_Summary | 0.648 | 0.007 | 0.658 | |
| BASiCS_TestDE | 2.726 | 0.147 | 2.907 | |
| BASiCS_VarThresholdSearchHVG_LVG | 0.160 | 0.020 | 0.181 | |
| BASiCS_VarianceDecomp | 0.086 | 0.007 | 0.094 | |
| BASiCS_showFit-BASiCS_Chain-method | 0.672 | 0.013 | 0.693 | |
| Summary-BASiCS_Chain-method | 0.159 | 0.019 | 0.180 | |
| colnames-BASiCS_Chain-method | 0.169 | 0.018 | 0.192 | |
| displayChainBASiCS-BASiCS_Chain-method | 0.161 | 0.021 | 0.183 | |
| displaySummaryBASiCS-BASiCS_Summary-method | 0.155 | 0.018 | 0.176 | |
| makeExampleBASiCS_Data | 0.077 | 0.001 | 0.077 | |
| newBASiCS_Chain | 1.268 | 0.007 | 1.283 | |
| newBASiCS_Data | 0.225 | 0.000 | 0.227 | |
| plot-BASiCS_Chain-method | 0.145 | 0.018 | 0.165 | |
| plot-BASiCS_Summary-method | 0.177 | 0.019 | 0.198 | |
| rownames-BASiCS_Chain-method | 0.195 | 0.021 | 0.226 | |
| subset-BASiCS_Chain-method | 0.179 | 0.022 | 0.206 | |