Back to Multiple platform build/check report for BioC 3.22:   simplified   long
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This page was generated on 2025-09-25 12:04 -0400 (Thu, 25 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4831
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4618
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4562
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4560
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 739/2334HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
flowcatchR 1.43.0  (landing page)
Federico Marini
Snapshot Date: 2025-09-24 13:45 -0400 (Wed, 24 Sep 2025)
git_url: https://git.bioconductor.org/packages/flowcatchR
git_branch: devel
git_last_commit: 68743ab
git_last_commit_date: 2025-04-15 10:35:15 -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  UNNEEDED, same version is already published
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for flowcatchR on nebbiolo2

To the developers/maintainers of the flowcatchR package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/flowcatchR.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: flowcatchR
Version: 1.43.0
Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:flowcatchR.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings flowcatchR_1.43.0.tar.gz
StartedAt: 2025-09-24 23:50:59 -0400 (Wed, 24 Sep 2025)
EndedAt: 2025-09-24 23:52:29 -0400 (Wed, 24 Sep 2025)
EllapsedTime: 90.1 seconds
RetCode: 0
Status:   OK  
CheckDir: flowcatchR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:flowcatchR.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings flowcatchR_1.43.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/flowcatchR.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘flowcatchR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘flowcatchR’ version ‘1.43.0’
* 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 ‘flowcatchR’ 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 ... NOTE
'library' or 'require' call to ‘EBImage’ which was already attached by Depends.
  Please remove these calls from your code.
* 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 ... NOTE
Non-topic package-anchored link(s) in Rd file 'preprocess.Frames.Rd':
  ‘[EBImage:morphology]{EBImage::opening()}’
  ‘[EBImage:morphology]{EBImage::closing()}’

See section 'Cross-references' in the 'Writing R Extensions' manual.
* 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/flowcatchR.Rcheck/00check.log’
for details.


Installation output

flowcatchR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL flowcatchR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘flowcatchR’ ...
** this is package ‘flowcatchR’ version ‘1.43.0’
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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 (flowcatchR)

Tests output


Example timings

flowcatchR.Rcheck/flowcatchR-Ex.timings

nameusersystemelapsed
Frames0.2370.0550.293
add.contours0.0000.0000.001
channel.Frames0.2130.0070.220
crop.Frames0.0700.0060.075
export.Frames0.0000.0010.000
export.particles0.0010.0000.000
inspect.Frames000
kinematics0.3690.0090.378
length.Frames0.0380.0230.061
link.particles0.0880.0020.090
matchTrajToParticles0.1750.0030.179
normalizeFrames1.4320.0801.512
particles0.0000.0000.001
penaltyFunctionGenerator0.0000.0000.001
plot.TrajectorySet0.1530.0000.153
plot2D.TrajectorySet0.2280.0130.241
preprocess.Frames0.3950.0000.395
read.Frames000
read.particles000
rotate.Frames0.2710.0000.272
select.Frames0.4800.0000.479
select.particles0.0180.0000.018
shinyFlow000
show-Frames-method0.0480.0000.049
show-KinematicsFeatures-method0.1490.0000.149
show-KinematicsFeaturesSet-method0.1790.0020.181
show-LinkedParticleSet-method0.130.000.13
show-ParticleSet-method0.0040.0000.005
show-TrajectorySet-method0.1600.0000.159
snap000
trajectories0.1530.0000.152