Back to Mac ARM64 build report for BioC 3.17
ABCDE[F]GHIJKLMNOPQRSTUVWXYZ

This page was generated on 2023-10-20 09:38:02 -0400 (Fri, 20 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson2macOS 12.6.1 Montereyarm644.3.1 (2023-06-16) -- "Beagle Scouts" 4347
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 711/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
flowClean 1.38.0  (landing page)
Kipper Fletez-Brant
Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/flowClean
git_branch: RELEASE_3_17
git_last_commit: 57ef364
git_last_commit_date: 2023-04-25 10:32:24 -0400 (Tue, 25 Apr 2023)
kjohnson2macOS 12.6.1 Monterey / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

CHECK results for flowClean on kjohnson2


To the developers/maintainers of the flowClean package:
- 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: 1.38.0
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_1.38.0.tar.gz
StartedAt: 2023-10-17 19:47:46 -0400 (Tue, 17 Oct 2023)
EndedAt: 2023-10-17 19:50:01 -0400 (Tue, 17 Oct 2023)
EllapsedTime: 134.7 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: flowClean.Rcheck
Warnings: 3

Command output

##############################################################################
##############################################################################
###
### 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_1.38.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/flowClean.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-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 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘flowClean/DESCRIPTION’ ... OK
* this is package ‘flowClean’ version ‘1.38.0’
* 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 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
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 documentation object 'clean':
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 documentation object 'clean':
  ‘announce’
Documented arguments not in \usage in documentation object 'clean':
  ‘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: '.local' is deprecated.
  Warning: '.local' is deprecated.
  Warning: '.local' is deprecated.
  Warning: '.local' is deprecated.
  Warning: '.local' is deprecated.
  Warning: 'description<-' is deprecated.
  Warning: '.local' is deprecated.
  Warning: '.local' is deprecated.
  Warning: 'description<-' is deprecated.
  Warning: '.local' is deprecated.
  Warning: '.local' is deprecated.
  Warning: 'description<-' is deprecated.
  Warning: '.local' is deprecated.
  Warning: 'description<-' is deprecated.
  Warning: '.local' is deprecated.
  Warning: 'description<-' is deprecated.
  Warning: '.local' is deprecated.
  Warning: 'description<-' is deprecated.
  Warning: '.local' is deprecated.
  Warning: 'description<-' is deprecated.
  Warning: '.local' is deprecated.
  Warning: 'description<-' is deprecated.
  Warning: '.local' is deprecated.
  Warning: 'description<-' is deprecated.
  Warning: '.local' is deprecated.
  Warning: 'description<-' is deprecated.
  Warning: '.local' is deprecated.
  Warning: '.local' is deprecated.
  Warning: 'description<-' is deprecated.
  Warning: '.local' is deprecated.
  Warning: 'description<-' 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 12.801  0.466  23.021
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... 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-3.17-bioc-mac-arm64/meat/flowClean.Rcheck/00check.log’
for details.



Installation output

flowClean.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/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
clean12.801 0.46623.021
synPerturbed0.4030.0220.753