Back to Multiple platform build/check report for BioC 3.20:   simplified   long
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This page was generated on 2024-12-23 12:07 -0500 (Mon, 23 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4744
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4487
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4515
kjohnson1macOS 13.6.6 Venturaarm644.4.2 (2024-10-31) -- "Pile of Leaves" 4467
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 724/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
flowBin 1.42.0  (landing page)
Kieran O'Neill
Snapshot Date: 2024-12-19 13:00 -0500 (Thu, 19 Dec 2024)
git_url: https://git.bioconductor.org/packages/flowBin
git_branch: RELEASE_3_20
git_last_commit: 58980d6
git_last_commit_date: 2024-10-29 09:49:41 -0500 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for flowBin on kjohnson1

To the developers/maintainers of the flowBin package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/flowBin.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: flowBin
Version: 1.42.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:flowBin.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings flowBin_1.42.0.tar.gz
StartedAt: 2024-12-20 19:35:18 -0500 (Fri, 20 Dec 2024)
EndedAt: 2024-12-20 19:36:46 -0500 (Fri, 20 Dec 2024)
EllapsedTime: 87.8 seconds
RetCode: 0
Status:   OK  
CheckDir: flowBin.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:flowBin.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings flowBin_1.42.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/flowBin.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: aarch64-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 Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘flowBin/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘flowBin’ version ‘1.42.0’
* 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 ‘flowBin’ 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 ... NOTE
Package in Depends field not imported from: ‘flowCore’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.getBinExpr.def : getBinFrame: no visible global function definition
  for ‘exprs<-’
.getBinExpr.def : getBinFrame: no visible global function definition
  for ‘exprs’
.getBinExpr.def : scaleData: no visible global function definition for
  ‘pData’
.getBinExpr.def : getOnePopExpr : extractOneTube : <anonymous>: no
  visible global function definition for ‘exprs’
.getBinExpr.def : getOnePopExpr : extractOneTube: no visible global
  function definition for ‘pData’
.getBinExpr.def : getOneBinMeds : <anonymous>: no visible global
  function definition for ‘median’
.getBinExpr.def : getOneBinMeds : <anonymous>: no visible global
  function definition for ‘exprs’
.getBinExpr.def : getOneBinMeds: no visible global function definition
  for ‘pData’
checkQNorm.func: no visible global function definition for ‘flowSet’
checkQNorm.func: no visible global function definition for ‘par’
checkQNorm.func: no visible binding for global variable ‘sd’
flowFPBin.def: no visible global function definition for ‘flowSet’
kMeansBin.def: no visible global function definition for ‘exprs’
kMeansBin.def: no visible global function definition for ‘pData’
kMeansBin.def: no visible global function definition for ‘kmeans’
mapBinsKNN.def : mapClustersKNN: no visible global function definition
  for ‘exprs’
mapBinsKNN.def: no visible global function definition for
  ‘capture.output’
mapBinsKNN.def: no visible global function definition for ‘parLapply’
medianFI: no visible global function definition for ‘median’
medianFIDist: no visible global function definition for ‘median’
proportionPositive: no visible global function definition for
  ‘quantile’
qnorm.func : normCol : <anonymous>: no visible global function
  definition for ‘exprs’
qnorm.func : normCol : getCol: no visible global function definition
  for ‘exprs’
qnorm.func : normCol : getCol: no visible global function definition
  for ‘runif’
qnorm.func : normCol : setCol: no visible global function definition
  for ‘exprs’
qnorm.func : normCol : setCol: no visible global function definition
  for ‘exprs<-’
checkQNorm,FlowSample-FlowSample: no visible global function definition
  for ‘flowSet’
checkQNorm,FlowSample-FlowSample: no visible global function definition
  for ‘par’
checkQNorm,FlowSample-FlowSample: no visible binding for global
  variable ‘sd’
flowFPBin,FlowSample: no visible global function definition for
  ‘flowSet’
getBinExpr,BinnedFlowSample : getBinFrame: no visible global function
  definition for ‘exprs<-’
getBinExpr,BinnedFlowSample : getBinFrame: no visible global function
  definition for ‘exprs’
getBinExpr,BinnedFlowSample : scaleData: no visible global function
  definition for ‘pData’
getBinExpr,BinnedFlowSample : getOnePopExpr : extractOneTube :
  <anonymous>: no visible global function definition for ‘exprs’
getBinExpr,BinnedFlowSample : getOnePopExpr : extractOneTube: no
  visible global function definition for ‘pData’
getBinExpr,BinnedFlowSample : getOneBinMeds : <anonymous>: no visible
  global function definition for ‘median’
getBinExpr,BinnedFlowSample : getOneBinMeds : <anonymous>: no visible
  global function definition for ‘exprs’
getBinExpr,BinnedFlowSample : getOneBinMeds: no visible global function
  definition for ‘pData’
kMeansBin,FlowSample: no visible global function definition for ‘exprs’
kMeansBin,FlowSample: no visible global function definition for ‘pData’
kMeansBin,FlowSample: no visible global function definition for
  ‘kmeans’
mapBinsKNN,FlowSample : mapClustersKNN: no visible global function
  definition for ‘exprs’
mapBinsKNN,FlowSample: no visible global function definition for
  ‘capture.output’
mapBinsKNN,FlowSample: no visible global function definition for
  ‘parLapply’
quantileNormalise,FlowSample : normCol : <anonymous>: no visible global
  function definition for ‘exprs’
quantileNormalise,FlowSample : normCol : getCol: no visible global
  function definition for ‘exprs’
quantileNormalise,FlowSample : normCol : getCol: no visible global
  function definition for ‘runif’
quantileNormalise,FlowSample : normCol : setCol: no visible global
  function definition for ‘exprs’
quantileNormalise,FlowSample : normCol : setCol: no visible global
  function definition for ‘exprs<-’
show,FlowSample: no visible global function definition for ‘str’
Undefined global functions or variables:
  capture.output exprs exprs<- flowSet kmeans median pData par
  parLapply quantile runif sd str
Consider adding
  importFrom("graphics", "par")
  importFrom("stats", "kmeans", "median", "quantile", "runif", "sd")
  importFrom("utils", "capture.output", "str")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... NOTE
Invalid package aliases in Rd file 'flowBin.Rd':
  ‘flowbin-package’
* 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 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
            user system elapsed
flowBin    5.373  0.049   5.424
getBinExpr 5.104  0.037   5.147
* 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 NOTEs
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/flowBin.Rcheck/00check.log’
for details.


Installation output

flowBin.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’
* installing *source* package ‘flowBin’ ...
** 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 (flowBin)

Tests output


Example timings

flowBin.Rcheck/flowBin-Ex.timings

nameusersystemelapsed
checkQNorm0.5170.0240.540
flowBin5.3730.0495.424
flowFPBin0.3410.0110.352
getBinExpr5.1040.0375.147
kMeansBin0.4490.0080.456
mapBinsKNN0.2590.0060.264
quantileNormalise0.4170.0150.435