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This page was generated on 2024-12-23 12:03 -0500 (Mon, 23 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4744
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4487
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4515
kjohnson1macOS 13.6.6 Venturaarm644.4.2 (2024-10-31) -- "Pile of Leaves" 4467
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 154/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BEARscc 1.26.0  (landing page)
Benjamin Schuster-Boeckler
Snapshot Date: 2024-12-19 13:00 -0500 (Thu, 19 Dec 2024)
git_url: https://git.bioconductor.org/packages/BEARscc
git_branch: RELEASE_3_20
git_last_commit: c921c5b
git_last_commit_date: 2024-10-29 10:25:23 -0500 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    ERROR  
palomino8Windows Server 2022 Datacenter / x64  OK    OK    ERROR    OK  
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    ERROR    OK  
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    ERROR    OK  


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: 1.26.0
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:BEARscc.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings BEARscc_1.26.0.tar.gz
StartedAt: 2024-12-19 20:21:35 -0500 (Thu, 19 Dec 2024)
EndedAt: 2024-12-19 20:28:50 -0500 (Thu, 19 Dec 2024)
EllapsedTime: 435.4 seconds
RetCode: 1
Status:   ERROR  
CheckDir: BEARscc.Rcheck
Warnings: NA

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:BEARscc.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings BEARscc_1.26.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/BEARscc.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘BEARscc/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BEARscc’ version ‘1.26.0’
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 code 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 ... ERROR
Running examples in ‘BEARscc-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: report_cell_metrics
> ### Title: Reports BEARscc metrics for cells.
> ### Aliases: report_cell_metrics calculate_cell_metrics
> ###   calculate_cell_metrics_by_cluster . rn
> ### Keywords: list
> 
> ### ** Examples
> 
> data(analysis_examples)
> 
> cell_scores.df <- report_cell_metrics(BEARscc_clusts.df, noise_consensus)
Error in doWithOneRestart(return(expr), restart) : bad error message
Calls: report_cell_metrics ... signal -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/BEARscc.Rcheck/00check.log’
for details.


Installation output

BEARscc.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL BEARscc
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.20-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 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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 
 14.408   0.598  14.944 

Example timings

BEARscc.Rcheck/BEARscc-Ex.timings

nameusersystemelapsed
BEARscc_examples0.0320.0010.033
analysis_examples0.0560.0030.059
cluster_consensus0.0420.0020.044
compute_consensus0.0690.0010.071
estimate_noiseparameters6.4010.2446.545