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This page was generated on 2024-02-21 11:35:52 -0500 (Wed, 21 Feb 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.2 Patched (2023-11-13 r85521) -- "Eye Holes" 4691
palomino4Windows Server 2022 Datacenterx644.3.2 (2023-10-31 ucrt) -- "Eye Holes" 4444
lconwaymacOS 12.7.1 Montereyx86_644.3.2 Patched (2023-11-01 r85457) -- "Eye Holes" 4465
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 149/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BEARscc 1.22.0  (landing page)
Benjamin Schuster-Boeckler
Snapshot Date: 2024-02-20 14:05:06 -0500 (Tue, 20 Feb 2024)
git_url: https://git.bioconductor.org/packages/BEARscc
git_branch: RELEASE_3_18
git_last_commit: 243e1c2
git_last_commit_date: 2023-10-24 11:02:36 -0500 (Tue, 24 Oct 2023)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here

CHECK results for BEARscc on nebbiolo2


To the developers/maintainers of the BEARscc package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BEARscc.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: BEARscc
Version: 1.22.0
Command: /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:BEARscc.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings BEARscc_1.22.0.tar.gz
StartedAt: 2024-02-20 20:20:51 -0500 (Tue, 20 Feb 2024)
EndedAt: 2024-02-20 20:25:04 -0500 (Tue, 20 Feb 2024)
EllapsedTime: 252.3 seconds
RetCode: 0
Status:   OK  
CheckDir: BEARscc.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:BEARscc.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings BEARscc_1.22.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/BEARscc.Rcheck’
* using R version 4.3.2 Patched (2023-11-13 r85521)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.3 LTS
* using session charset: UTF-8
* checking for file ‘BEARscc/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BEARscc’ version ‘1.22.0’
* 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 loading without being on the library search path ... 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 6.712  0.124   6.748
* 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 ...
  ‘BEARscc.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: OK


Installation output

BEARscc.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD INSTALL BEARscc
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.18-bioc/R/site-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 4.3.2 Patched (2023-11-13 r85521) -- "Eye Holes"
Copyright (C) 2023 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..."
[ FAIL 0 | WARN 13 | SKIP 0 | PASS 25 ]

[ FAIL 0 | WARN 13 | SKIP 0 | PASS 25 ]
> 
> proc.time()
   user  system elapsed 
 16.621   0.577  17.134 

Example timings

BEARscc.Rcheck/BEARscc-Ex.timings

nameusersystemelapsed
BEARscc_examples0.0300.0030.035
analysis_examples0.0380.0030.042
cluster_consensus0.0450.0050.048
compute_consensus0.7000.0310.731
estimate_noiseparameters6.7120.1246.748
report_cell_metrics0.4160.0240.440
report_cluster_metrics0.7590.0080.761
simulate_replicates4.8590.0724.931