Package: MetaCyto

Version: 1.6.0

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_1.6.0.tar.gz

StartedAt: 2019-10-16 04:25:45 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 04:32:39 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 413.9 seconds

RetCode: 0

Status:  OK

CheckDir: MetaCyto.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running 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_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/MetaCyto.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.6.0’
* 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 : : 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   79.103 22.908 102.031
labelCluster        70.428 22.359  92.843
flowSOM.MC          19.946  8.464  28.438
searchCluster.batch 20.182  3.531  23.714
searchCluster        7.000  1.734   8.734
densityPlot          6.001  1.880   7.882
clusterStats         5.599  1.778   7.378
* 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-3.9-bioc/meat/MetaCyto.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL MetaCyto
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘MetaCyto’ ...
** using staged installation
** 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 from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (MetaCyto)

name	user	system	elapsed
autoCluster.batch	79.103	22.908	102.031
clusterStats	5.599	1.778	7.378
collectData	0.050	0.004	0.057
densityPlot	6.001	1.880	7.882
fcsInfoParser	0.168	0.004	0.172
filterLabels	0.002	0.000	0.003
findCutoff	1.290	0.445	1.735
flowHC	3.379	0.285	3.664
flowSOM.MC	19.946	8.464	28.438
glmAnalysis	0.558	0.030	0.593
labelCluster	70.428	22.359	92.843
labelSummary	0.697	0.022	0.719
markerFinder	0.045	0.002	0.048
metaAnalysis	0.157	0.009	0.167
nameUpdator	1.718	0.099	1.817
panelSummary	0.034	0.004	0.039
plotGA	0.917	0.045	0.962
preprocessing	0.727	0.008	0.735
preprocessing.batch	1.642	0.036	1.679
sampleInfoParser	0.005	0.000	0.005
searchCluster	7.000	1.734	8.734
searchCluster.batch	20.182	3.531	23.714
set2Frame	0.158	0.008	0.166