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CHECK report for MetaCyto on veracruz1

This page was generated on 2018-04-12 13:46:05 -0400 (Thu, 12 Apr 2018).

Package 821/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MetaCyto 1.4.0
Zicheng Hu
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/MetaCyto
Branch: RELEASE_3_6
Last Commit: ecc01f6
Last Changed Date: 2018-01-24 16:58:43 -0400 (Wed, 24 Jan 2018)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: MetaCyto
Version: 1.4.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings MetaCyto_1.4.0.tar.gz
StartedAt: 2018-04-12 06:05:40 -0400 (Thu, 12 Apr 2018)
EndedAt: 2018-04-12 06:11:03 -0400 (Thu, 12 Apr 2018)
EllapsedTime: 322.8 seconds
RetCode: 0
Status:  OK 
CheckDir: MetaCyto.Rcheck
Warnings: 0

Command output

##############################################################################
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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings MetaCyto_1.4.0.tar.gz
###
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##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/MetaCyto.Rcheck’
* using R version 3.4.4 (2018-03-15)
* 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 ‘1.4.0’
* 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 loading without being on the library search path ... 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
labelCluster        73.058  7.629  82.493
autoCluster.batch   57.374 11.834  71.751
searchCluster.batch 22.760  2.151  25.517
flowSOM.MC          12.963  3.314  16.770
searchCluster        7.419  0.553   8.138
densityPlot          4.421  0.845   5.405
clusterStats         4.255  0.839   5.239
* 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-3.6-bioc/meat/MetaCyto.Rcheck/00check.log’
for details.



Installation output

MetaCyto.Rcheck/00install.out

* installing *source* package ‘MetaCyto’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (MetaCyto)

Tests output


Example timings

MetaCyto.Rcheck/MetaCyto-Ex.timings

nameusersystemelapsed
autoCluster.batch57.37411.83471.751
clusterStats4.2550.8395.239
collectData0.0920.0010.093
densityPlot4.4210.8455.405
fcsInfoParser0.0910.0010.093
filterLabels0.0020.0010.002
findCutoff1.0650.2511.361
flowHC2.1200.1172.272
flowSOM.MC12.963 3.31416.770
glmAnalysis0.4950.0090.508
labelCluster73.058 7.62982.493
labelSummary0.4910.0030.500
markerFinder0.0240.0010.025
metaAnalysis0.1190.0030.124
nameUpdator1.2900.0241.335
panelSummary0.0360.0010.037
plotGA1.1420.0051.162
preprocessing0.4790.0080.496
preprocessing.batch1.2750.0191.318
sampleInfoParser0.0050.0000.005
searchCluster7.4190.5538.138
searchCluster.batch22.760 2.15125.517
set2Frame0.1060.0100.117