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CHECK report for MetaCyto on celaya2

This page was generated on 2020-01-16 13:49:43 -0500 (Thu, 16 Jan 2020).

Package 996/1818HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MetaCyto 1.9.0
Zicheng Hu
Snapshot Date: 2020-01-15 16:46:30 -0500 (Wed, 15 Jan 2020)
URL: https://git.bioconductor.org/packages/MetaCyto
Branch: master
Last Commit: dec108c
Last Changed Date: 2019-10-29 13:42:34 -0500 (Tue, 29 Oct 2019)
malbec2 Linux (Ubuntu 18.04.3 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: MetaCyto
Version: 1.9.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:MetaCyto.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings MetaCyto_1.9.0.tar.gz
StartedAt: 2020-01-16 06:14:40 -0500 (Thu, 16 Jan 2020)
EndedAt: 2020-01-16 06:23:44 -0500 (Thu, 16 Jan 2020)
EllapsedTime: 544.0 seconds
RetCode: 0
Status:  OK 
CheckDir: MetaCyto.Rcheck
Warnings: 0

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:MetaCyto.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings MetaCyto_1.9.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/MetaCyto.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MetaCyto/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MetaCyto’ version ‘1.9.0’
* 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 ‘MetaCyto’ 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
collectData: no visible binding for global variable ‘parameter_name’
collectData: no visible binding for global variable ‘value’
panelSummary: no visible binding for global variable ‘antibodies’
panelSummary: no visible binding for global variable ‘value’
plotGA: no visible binding for global variable ‘lower’
plotGA: no visible binding for global variable ‘upper’
searchCluster : <anonymous>: no visible binding for global variable
  ‘triS’
Undefined global functions or variables:
  antibodies lower parameter_name triS upper value
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                       user system elapsed
autoCluster.batch   107.871 38.811 146.706
labelCluster         92.408 37.353 129.826
searchCluster.batch  27.017  6.394  33.446
flowSOM.MC           21.304  7.802  29.271
searchCluster         9.634  3.119  12.751
densityPlot           8.091  3.137  11.229
clusterStats          7.773  2.617  10.390
* 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 NOTE
See
  ‘/Users/biocbuild/bbs-3.11-bioc/meat/MetaCyto.Rcheck/00check.log’
for details.



Installation output

MetaCyto.Rcheck/00install.out

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL MetaCyto
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘MetaCyto’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import ‘ncdfFlow::filter’ by ‘dplyr::filter’ when loading ‘CytoML’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import ‘ncdfFlow::filter’ by ‘dplyr::filter’ when loading ‘CytoML’
** testing if installed package can be loaded from final location
Warning: replacing previous import ‘ncdfFlow::filter’ by ‘dplyr::filter’ when loading ‘CytoML’
** testing if installed package keeps a record of temporary installation path
* DONE (MetaCyto)

Tests output


Example timings

MetaCyto.Rcheck/MetaCyto-Ex.timings

nameusersystemelapsed
autoCluster.batch107.871 38.811146.706
clusterStats 7.773 2.61710.390
collectData0.0590.0040.065
densityPlot 8.091 3.13711.229
fcsInfoParser0.1360.0060.143
filterLabels0.0030.0010.003
findCutoff1.5470.7612.307
flowHC3.9180.3024.219
flowSOM.MC21.304 7.80229.271
glmAnalysis0.5060.0210.530
labelCluster 92.408 37.353129.826
labelSummary0.6710.0340.704
markerFinder0.0340.0020.036
metaAnalysis0.1850.0080.194
nameUpdator1.6540.0781.732
panelSummary0.0320.0030.035
plotGA0.9340.0210.955
preprocessing0.7750.0070.782
preprocessing.batch2.1310.0412.174
sampleInfoParser0.0050.0010.005
searchCluster 9.634 3.11912.751
searchCluster.batch27.017 6.39433.446
set2Frame0.1540.0080.161