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CHECK report for BEARscc on malbec1

This page was generated on 2020-08-07 11:34:51 -0400 (Fri, 07 Aug 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE BEARscc PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 129/1882HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BEARscc 1.9.1
Benjamin Schuster-Boeckler
Snapshot Date: 2020-08-06 14:50:46 -0400 (Thu, 06 Aug 2020)
URL: https://git.bioconductor.org/packages/BEARscc
Branch: master
Last Commit: 3860d28
Last Changed Date: 2020-06-02 23:17:57 -0400 (Tue, 02 Jun 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: BEARscc
Version: 1.9.1
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:BEARscc.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings BEARscc_1.9.1.tar.gz
StartedAt: 2020-08-07 03:36:06 -0400 (Fri, 07 Aug 2020)
EndedAt: 2020-08-07 03:39:57 -0400 (Fri, 07 Aug 2020)
EllapsedTime: 230.3 seconds
RetCode: 0
Status:  OK 
CheckDir: BEARscc.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:BEARscc.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings BEARscc_1.9.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/BEARscc.Rcheck’
* using R version 4.0.2 (2020-06-22)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BEARscc/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BEARscc’ version ‘1.9.1’
* 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 ‘BEARscc’ 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                           user system elapsed
estimate_noiseparameters 13.476  0.116  11.701
simulate_replicates       7.716  0.000   7.727
* 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: OK


Installation output

BEARscc.Rcheck/00install.out

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### Running command:
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###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL BEARscc
###
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* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/library’
* installing *source* package ‘BEARscc’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (BEARscc)

Tests output

BEARscc.Rcheck/tests/testthat.Rout


R version 4.0.2 (2020-06-22) -- "Taking Off Again"
Copyright (C) 2020 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(BEARscc)
> 
> test_check("BEARscc")

[1] "Running BEARscc on example data to test for correct installation."

[1] "Fitting parameter alpha to establish spike-in derived noise model."
[1] "Estimating error for spike-ins with alpha = 0"
[1] "Estimating error for spike-ins with alpha = 0.25"
[1] "Estimating error for spike-ins with alpha = 0.5"
[1] "Estimating error for spike-ins with alpha = 0.75"
[1] "Estimating error for spike-ins with alpha = 1"
[1] "There are adequate spike-in drop-outs to build the drop-out model. Estimating the drop-out model now."

[1] "Injecting noise for testing..."
[1] "Creating a simulated replicated counts matrix: 1."
[1] "Creating a simulated replicated counts matrix: 2."
[1] "Creating a simulated replicated counts matrix: 3."

[1] "Creating consensus matrix for testing..."

[1] "Computing cluster and cell metrics for testing..."
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 25 | SKIPPED: 0 | WARNINGS: 13 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 22.524   0.344  21.697 

Example timings

BEARscc.Rcheck/BEARscc-Ex.timings

nameusersystemelapsed
BEARscc_examples0.0280.0040.034
analysis_examples0.0400.0000.042
cluster_consensus0.0440.0000.047
compute_consensus0.0880.0000.090
estimate_noiseparameters13.476 0.11611.701
report_cell_metrics0.4440.0080.453
report_cluster_metrics1.0480.0280.993
simulate_replicates7.7160.0007.727