Back to Multiple platform build/check report for BioC 3.22:   simplified   long
AB[C]DEFGHIJKLMNOPQRSTUVWXYZ

This page was generated on 2025-08-16 12:04 -0400 (Sat, 16 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4818
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4596
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4538
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4535
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 487/2317HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cyanoFilter 1.17.0  (landing page)
Oluwafemi Olusoji
Snapshot Date: 2025-08-15 13:45 -0400 (Fri, 15 Aug 2025)
git_url: https://git.bioconductor.org/packages/cyanoFilter
git_branch: devel
git_last_commit: b7725b6
git_last_commit_date: 2025-04-15 12:25:42 -0400 (Tue, 15 Apr 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  NO, package depends on 'flowCore' which is only available as a source package that needs compilation
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    OK    OK  NO, package depends on 'flowCore' which is only available as a source package that needs compilation
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for cyanoFilter on lconway

To the developers/maintainers of the cyanoFilter package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/cyanoFilter.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: cyanoFilter
Version: 1.17.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:cyanoFilter.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings cyanoFilter_1.17.0.tar.gz
StartedAt: 2025-08-15 20:10:13 -0400 (Fri, 15 Aug 2025)
EndedAt: 2025-08-15 20:12:04 -0400 (Fri, 15 Aug 2025)
EllapsedTime: 111.7 seconds
RetCode: 0
Status:   OK  
CheckDir: cyanoFilter.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:cyanoFilter.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings cyanoFilter_1.17.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/cyanoFilter.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘cyanoFilter/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘cyanoFilter’ version ‘1.17.0’
* 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 ‘cyanoFilter’ 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 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
           user system elapsed
gateFunc 11.383  0.629   9.505
* 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: OK


Installation output

cyanoFilter.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘cyanoFilter’ ...
** this is package ‘cyanoFilter’ version ‘1.17.0’
** 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 (cyanoFilter)

Tests output


Example timings

cyanoFilter.Rcheck/cyanoFilter-Ex.timings

nameusersystemelapsed
MarginEvents0.8210.0750.906
PhytoFilter0.6730.0450.729
PhytopFilter0.6970.0540.760
accTest0.4710.0320.507
accuracy0.4320.0240.459
cellmargin0.3590.0290.392
clusterExtract0.9040.0390.950
clusterExtractp0.9250.0410.976
debrisNc0.5880.0480.644
fullFlowframe-MarginEvents-method0.3480.0300.384
fullFlowframe-PhytopFilter-method0.7200.0510.783
fullFlowframe0.3790.0380.423
gateFunc11.383 0.629 9.505
ggpairsDens3.6740.1313.824
ggplotDens0.5650.0270.596
ggplotDens20.8870.0390.933
goodfcs0.0620.0100.072
is.DebrisFilter000
is.MarginEvents000
is.PhytopFilter0.0000.0000.001
is.flowFrame0.0000.0000.001
is.flowSet0.0010.0000.000
lnTrans0.2690.0190.290
newFlowframe0.2340.0580.296
nona0.1180.0080.126
noneg0.1800.0090.192
oneDgate0.2380.0520.295
pairsPlot1.9400.1632.123
pigmentGate0.2840.0500.339
reducedFlowframe-MarginEvents-method0.3130.0230.340
reducedFlowframe0.3370.0300.371
retain0.0230.0020.025
rowNumbers0.2220.0540.279
summaries-DebrisFilter-method0.3370.0290.373
summaries-MarginEvents-method0.3430.0210.368
summaries-PhytopFilter-method0.6730.0400.722
summaries0.3220.0230.348