Package: MetaCyto

Version: 1.2.1

Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:MetaCyto.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings MetaCyto_1.2.1.tar.gz

StartedAt: 2018-10-16 01:49:25 -0400 (Tue, 16 Oct 2018)

EndedAt: 2018-10-16 01:53:02 -0400 (Tue, 16 Oct 2018)

EllapsedTime: 217.1 seconds

RetCode: 0

Status:  OK

CheckDir: MetaCyto.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:MetaCyto.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings MetaCyto_1.2.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/MetaCyto.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-pc-linux-gnu (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 ‘1.2.1’
* 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   51.948  7.544  59.618
labelCluster        46.392  3.796  50.250
searchCluster.batch 13.728  0.948  14.683
flowSOM.MC          10.268  0.032  10.319
searchCluster        4.664  0.732   5.402
* 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
  ‘/home/biocbuild/bbs-3.7-bioc/meat/MetaCyto.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL MetaCyto
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* installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/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	51.948	7.544	59.618
clusterStats	3.948	0.476	4.429
collectData	0.036	0.000	0.055
densityPlot	4.372	0.536	4.916
fcsInfoParser	0.124	0.000	0.142
filterLabels	0.004	0.000	0.002
findCutoff	0.976	0.216	1.192
flowHC	1.484	0.056	1.540
flowSOM.MC	10.268	0.032	10.319
glmAnalysis	0.412	0.004	0.437
labelCluster	46.392	3.796	50.250
labelSummary	0.324	0.000	0.328
markerFinder	0.020	0.000	0.019
metaAnalysis	0.068	0.000	0.071
nameUpdator	0.944	0.004	0.948
panelSummary	0.016	0.000	0.053
plotGA	0.452	0.004	0.456
preprocessing	0.336	0.000	0.337
preprocessing.batch	0.960	0.004	0.966
sampleInfoParser	0.008	0.000	0.008
searchCluster	4.664	0.732	5.402
searchCluster.batch	13.728	0.948	14.683
set2Frame	0.124	0.000	0.125