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This page was generated on 2024-03-04 11:39:40 -0500 (Mon, 04 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_64R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" 4676
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2024-01-14 r85805 ucrt) -- "Unsuffered Consequences" 4414
merida1macOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" 4441
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-01-16 r85812) -- "Unsuffered Consequences" 4417
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 1505/2251HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PeacoQC 1.13.0  (landing page)
Annelies Emmaneel
Snapshot Date: 2024-03-01 14:00:22 -0500 (Fri, 01 Mar 2024)
git_url: https://git.bioconductor.org/packages/PeacoQC
git_branch: devel
git_last_commit: 7c60c40
git_last_commit_date: 2023-10-24 11:23:07 -0500 (Tue, 24 Oct 2023)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  

CHECK results for PeacoQC on merida1


To the developers/maintainers of the PeacoQC package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/PeacoQC.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: PeacoQC
Version: 1.13.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:PeacoQC.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings PeacoQC_1.13.0.tar.gz
StartedAt: 2024-03-02 08:20:47 -0500 (Sat, 02 Mar 2024)
EndedAt: 2024-03-02 08:25:38 -0500 (Sat, 02 Mar 2024)
EllapsedTime: 290.4 seconds
RetCode: 0
Status:   OK  
CheckDir: PeacoQC.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:PeacoQC.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings PeacoQC_1.13.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/PeacoQC.Rcheck’
* using R Under development (unstable) (2024-01-16 r85808)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘PeacoQC/DESCRIPTION’ ... OK
* this is package ‘PeacoQC’ version ‘1.13.0’
* package encoding: UTF-8
* 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 ‘PeacoQC’ 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 ... NOTE
BuildBackgroundQCPlot: no visible binding for global variable ‘x_min’
BuildBackgroundQCPlot: no visible binding for global variable ‘x_max’
BuildBackgroundQCPlot: no visible binding for global variable ‘y_min’
BuildBackgroundQCPlot: no visible binding for global variable ‘y_max’
BuildBackgroundQCPlot: no visible binding for global variable
  ‘fill_blocks’
BuildChannelPlots: no visible binding for global variable ‘Cells’
BuildManualPartPlot: no visible binding for global variable ‘minimum’
BuildManualPartPlot: no visible binding for global variable ‘x_min’
BuildManualPartPlot: no visible binding for global variable ‘x_max’
BuildManualPartPlot: no visible binding for global variable ‘y_min’
BuildManualPartPlot: no visible binding for global variable ‘y_max’
BuildPeaksPlot: no visible binding for global variable ‘Bin’
BuildPeaksPlot: no visible binding for global variable ‘Peak’
BuildPeaksPlot: no visible binding for global variable ‘Cluster’
BuildTimePlot: no visible binding for global variable ‘x_min’
BuildTimePlot: no visible binding for global variable ‘x_max’
BuildTimePlot: no visible binding for global variable ‘y_min’
BuildTimePlot: no visible binding for global variable ‘y_max’
BuildTimePlot: no visible binding for global variable ‘fill_blocks’
Undefined global functions or variables:
  Bin Cells Cluster Peak fill_blocks minimum x_max x_min y_max y_min
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
PlotPeacoQC    28.494  0.420  34.479
PeacoQC        13.053  0.398  15.814
PeacoQCHeatmap 12.349  0.135  14.918
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... 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-3.19-bioc/meat/PeacoQC.Rcheck/00check.log’
for details.



Installation output

PeacoQC.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL PeacoQC
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘PeacoQC’ ...
** using staged installation
** R
** 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 (PeacoQC)

Tests output


Example timings

PeacoQC.Rcheck/PeacoQC-Ex.timings

nameusersystemelapsed
PeacoQC13.053 0.39815.814
PeacoQCHeatmap12.349 0.13514.918
PlotPeacoQC28.494 0.42034.479
RemoveDoublets0.0730.0070.095
RemoveMargins0.1640.0250.221