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This page was generated on 2024-04-17 11:37:44 -0400 (Wed, 17 Apr 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4676
palomino4Windows Server 2022 Datacenterx644.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" 4414
merida1macOS 12.7.1 Montereyx86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4437
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 727/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
flowDensity 1.36.1  (landing page)
Mehrnoush Malek
Snapshot Date: 2024-04-15 14:05:01 -0400 (Mon, 15 Apr 2024)
git_url: https://git.bioconductor.org/packages/flowDensity
git_branch: RELEASE_3_18
git_last_commit: e159b7d8
git_last_commit_date: 2023-10-27 18:14:19 -0400 (Fri, 27 Oct 2023)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here

CHECK results for flowDensity on merida1


To the developers/maintainers of the flowDensity package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/flowDensity.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: flowDensity
Version: 1.36.1
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:flowDensity.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings flowDensity_1.36.1.tar.gz
StartedAt: 2024-04-16 02:53:56 -0400 (Tue, 16 Apr 2024)
EndedAt: 2024-04-16 02:55:57 -0400 (Tue, 16 Apr 2024)
EllapsedTime: 120.9 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: flowDensity.Rcheck
Warnings: 4

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:flowDensity.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings flowDensity_1.36.1.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.18-bioc/meat/flowDensity.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: x86_64-apple-darwin20 (64-bit)
* 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 ‘flowDensity/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘flowDensity’ version ‘1.36.1’
* 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 ‘flowDensity’ can be installed ... OK
* checking installed package size ... OK
* checking package 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 ... WARNING
checkRd: (7) deGate.Rd:126: Invalid email address: <mmalekes@bccrc.ca>
checkRd: (7) getPeaks.Rd:55: Invalid email address: <mmalekes@bccrc.ca>
checkRd: (7) getflowFrame.Rd:23: Invalid email address: <jtaghiyar@bccrc.ca>
checkRd: (7) nmRemove.Rd:37: Invalid email address: <jtaghiyar@bccrc.ca>
checkRd: (7) nmRemove.Rd:38: Invalid email address: <mmalekes@bccrc.ca>
checkRd: (7) notSubFrame.Rd:41: Invalid email address: <mmalekes@bccrc.ca>
checkRd: (7) plotDens.Rd:89: Invalid email address: <mmalekes@bccrc.ca>
checkRd: (7) plotDens.Rd:90: Invalid email address: <jtaghiyar@bccrc.ca>
* checking Rd metadata ... OK
* checking Rd cross-references ... WARNING
Missing link or links in documentation object 'deGate.Rd':
  ‘flowDensity’

Missing link or links in documentation object 'getPeaks.Rd':
  ‘flowDensity’

See section 'Cross-references' in the 'Writing R Extensions' manual.
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘flowDensity’
Undocumented S4 methods:
  generic 'flowDensity' and siglist 'CellPopulation,ANY,logical'
  generic 'flowDensity' and siglist 'flowFrame,ANY,logical'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... WARNING
Files in the 'vignettes' directory newer than all files in 'inst/doc':
  ‘flowDensity.Rmd’
Files named as vignettes but with no recognized vignette engine:
   ‘vignettes/flowDensity.Rmd’
(Is a VignetteBuilder field missing?)
* checking examples ... OK
* checking PDF version of manual ... OK
* DONE

Status: 4 WARNINGs
See
  ‘/Users/biocbuild/bbs-3.18-bioc/meat/flowDensity.Rcheck/00check.log’
for details.



Installation output

flowDensity.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL flowDensity
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library’
* installing *source* package ‘flowDensity’ ...
** 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 (flowDensity)

Tests output


Example timings

flowDensity.Rcheck/flowDensity-Ex.timings

nameusersystemelapsed
CellPopulation-class0.0020.0020.004
deGate0.2000.0350.273
getPeaks0.0450.0090.059
getflowFrame0.0990.0100.115
nmRemove0.2930.0310.366
notSubFrame0.1170.0130.132
plotDens0.1820.0250.259