Package: MetaCyto

Version: 1.4.1

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_1.4.1.tar.gz

StartedAt: 2019-04-16 01:07:55 -0400 (Tue, 16 Apr 2019)

EndedAt: 2019-04-16 01:13:13 -0400 (Tue, 16 Apr 2019)

EllapsedTime: 317.5 seconds

RetCode: 0

Status:  OK

CheckDir: MetaCyto.Rcheck

Warnings: 0

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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_1.4.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/MetaCyto.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘1.4.1’
* 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 or elapsed time > 5s
                      user system elapsed
autoCluster.batch   68.144 12.203  81.302
labelCluster        60.418 13.104  74.245
flowSOM.MC          16.179  4.711  21.147
searchCluster.batch 17.277  2.676  20.145
searchCluster        5.616  0.654   6.327
densityPlot          5.257  0.817   6.128
clusterStats         5.236  0.515   5.805
* 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-3.8-bioc/meat/MetaCyto.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL MetaCyto
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘MetaCyto’ ...
** R
** 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
* DONE (MetaCyto)

name	user	system	elapsed
autoCluster.batch	68.144	12.203	81.302
clusterStats	5.236	0.515	5.805
collectData	0.042	0.021	0.064
densityPlot	5.257	0.817	6.128
fcsInfoParser	0.116	0.002	0.120
filterLabels	0.002	0.000	0.002
findCutoff	1.064	0.255	1.324
flowHC	2.445	0.131	2.591
flowSOM.MC	16.179	4.711	21.147
glmAnalysis	0.426	0.006	0.435
labelCluster	60.418	13.104	74.245
labelSummary	0.614	0.011	0.626
markerFinder	0.027	0.002	0.029
metaAnalysis	0.091	0.002	0.095
nameUpdator	1.525	0.055	1.591
panelSummary	0.023	0.002	0.024
plotGA	0.747	0.005	0.754
preprocessing	0.644	0.004	0.650
preprocessing.batch	1.524	0.017	1.560
sampleInfoParser	0.003	0.000	0.003
searchCluster	5.616	0.654	6.327
searchCluster.batch	17.277	2.676	20.145
set2Frame	0.114	0.006	0.120