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CHECK report for flowUtils on machv2

This page was generated on 2020-10-17 11:58:30 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE flowUtils PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 630/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
flowUtils 1.52.0
Josef Spidlen
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/flowUtils
Branch: RELEASE_3_11
Last Commit: f79c522
Last Changed Date: 2020-04-27 14:14:17 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository

Summary

Package: flowUtils
Version: 1.52.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:flowUtils.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings flowUtils_1.52.0.tar.gz
StartedAt: 2020-10-17 01:14:56 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 01:16:12 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 75.9 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: flowUtils.Rcheck
Warnings: 1

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:flowUtils.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings flowUtils_1.52.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/flowUtils.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘flowUtils/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘flowUtils’ version ‘1.52.0’
* 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 ‘flowUtils’ 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 ... 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 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.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
* 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: 1 WARNING
See
  ‘/Users/biocbuild/bbs-3.11-bioc/meat/flowUtils.Rcheck/00check.log’
for details.



Installation output

flowUtils.Rcheck/00install.out

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL flowUtils
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘flowUtils’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
No methods found in package ‘flowCore’ for requests: ‘action’, ‘assign’, ‘Data’, ‘gate’, ‘tree’ when loading ‘flowUtils’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
No methods found in package ‘flowCore’ for requests: ‘action’, ‘assign’, ‘Data’, ‘gate’, ‘tree’ when loading ‘flowUtils’
** testing if installed package can be loaded from final location
No methods found in package ‘flowCore’ for requests: ‘action’, ‘assign’, ‘Data’, ‘gate’, ‘tree’ when loading ‘flowUtils’
** testing if installed package keeps a record of temporary installation path
* DONE (flowUtils)

Tests output


Example timings

flowUtils.Rcheck/flowUtils-Ex.timings

nameusersystemelapsed
read.gatingML0.8750.0300.909
testGatingMLCompliance0.0000.0010.001
write.gatingML1.7940.0441.839