Back to Multiple platform build/check report for BioC 3.20:   simplified   long
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This page was generated on 2024-07-13 11:41 -0400 (Sat, 13 Jul 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4677
palomino6Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4416
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4444
kjohnson3macOS 13.6.5 Venturaarm644.4.1 (2024-06-14) -- "Race for Your Life" 4393
palomino8Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4373
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 712/2243HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
flowClean 1.43.0  (landing page)
Kipper Fletez-Brant
Snapshot Date: 2024-07-12 14:00 -0400 (Fri, 12 Jul 2024)
git_url: https://git.bioconductor.org/packages/flowClean
git_branch: devel
git_last_commit: b8d2bc7
git_last_commit_date: 2024-04-30 10:36:50 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino6Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.6.5 Ventura / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  


CHECK results for flowClean on lconway

To the developers/maintainers of the flowClean package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/flowClean.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: flowClean
Version: 1.43.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:flowClean.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings flowClean_1.43.0.tar.gz
StartedAt: 2024-07-12 20:32:25 -0400 (Fri, 12 Jul 2024)
EndedAt: 2024-07-12 20:33:50 -0400 (Fri, 12 Jul 2024)
EllapsedTime: 84.4 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: flowClean.Rcheck
Warnings: 3

Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:flowClean.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings flowClean_1.43.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/flowClean.Rcheck’
* using R version 4.4.1 (2024-06-14)
* 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 ‘flowClean/DESCRIPTION’ ... OK
* this is package ‘flowClean’ version ‘1.43.0’
* 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 ‘flowClean’ 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 ... NOTE
clean: no visible global function definition for ‘runif’
clean: no visible global function definition for ‘png’
clean: no visible global function definition for ‘dev.off’
diagnosticPlot: no visible global function definition for ‘points’
diagnosticPlot: no visible global function definition for ‘abline’
makeFCS: no visible global function definition for ‘new’
make_pops : <anonymous>: no visible global function definition for
  ‘quantile’
make_pops : <anonymous>: no visible global function definition for
  ‘median’
Undefined global functions or variables:
  abline dev.off median new png points quantile runif
Consider adding
  importFrom("grDevices", "dev.off", "png")
  importFrom("graphics", "abline", "points")
  importFrom("methods", "new")
  importFrom("stats", "median", "quantile", "runif")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from Rd file 'clean.Rd':
clean
  Code: function(fF, vectMarkers, filePrefixWithDir, ext, binSize =
                 0.01, nCellCutoff = 500, announce = TRUE, cutoff =
                 "median", diagnostic = FALSE, fcMax = 1.3,
                 returnVector = FALSE, nstable = 5)
  Docs: function(fF, vectMarkers, filePrefixWithDir, ext, binSize =
                 0.01, nCellCutoff = 500, announce = TRUE, cutoff =
                 "median", diagnostic = FALSE, fcMax = 1.3)
  Argument names in code not in docs:
    returnVector nstable

* checking Rd \usage sections ... WARNING
Duplicated \argument entries in Rd file 'clean.Rd':
  ‘announce’
Documented arguments not in \usage in Rd file 'clean.Rd':
  ‘returnVector’ ‘nstable’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... WARNING
Found the following significant warnings:

  Warning in .local(object, ...) : '.local' is deprecated.
  Warning in .local(object, ...) : '.local' is deprecated.
  Warning in .local(object, ...) : '.local' is deprecated.
  Warning in .local(object, ...) : '.local' is deprecated.
  Warning in .local(object, ...) : '.local' is deprecated.
  Warning in .local(object, ...) : '.local' is deprecated.
  Warning in .local(object, ...) : '.local' is deprecated.
  Warning in .local(object, ...) : '.local' is deprecated.
  Warning in .local(object, ...) : '.local' is deprecated.
  Warning in .local(object, ...) : '.local' is deprecated.
  Warning in .local(object, ...) : '.local' is deprecated.
  Warning in .local(object, ...) : '.local' is deprecated.
  Warning in .local(object, ...) : '.local' is deprecated.
  Warning in .local(object, ...) : '.local' is deprecated.
  Warning in .local(object, ...) : '.local' is deprecated.
  Warning in .local(object, ...) : '.local' is deprecated.
  Warning in .local(object, ...) : '.local' is deprecated.
  Warning in .local(object, ...) : '.local' is deprecated.
  Warning in .local(object, ...) : '.local' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Examples with CPU (user + system) or elapsed time > 5s
        user system elapsed
clean 11.907  0.983  13.001
* 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: 3 WARNINGs, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/flowClean.Rcheck/00check.log’
for details.


Installation output

flowClean.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘flowClean’ ...
** 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 (flowClean)

Tests output


Example timings

flowClean.Rcheck/flowClean-Ex.timings

nameusersystemelapsed
clean11.907 0.98313.001
synPerturbed0.3780.0130.394