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

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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.

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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/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)

name	user	system	elapsed
autoCluster.batch	107.871	38.811	146.706
clusterStats	7.773	2.617	10.390
collectData	0.059	0.004	0.065
densityPlot	8.091	3.137	11.229
fcsInfoParser	0.136	0.006	0.143
filterLabels	0.003	0.001	0.003
findCutoff	1.547	0.761	2.307
flowHC	3.918	0.302	4.219
flowSOM.MC	21.304	7.802	29.271
glmAnalysis	0.506	0.021	0.530
labelCluster	92.408	37.353	129.826
labelSummary	0.671	0.034	0.704
markerFinder	0.034	0.002	0.036
metaAnalysis	0.185	0.008	0.194
nameUpdator	1.654	0.078	1.732
panelSummary	0.032	0.003	0.035
plotGA	0.934	0.021	0.955
preprocessing	0.775	0.007	0.782
preprocessing.batch	2.131	0.041	2.174
sampleInfoParser	0.005	0.001	0.005
searchCluster	9.634	3.119	12.751
searchCluster.batch	27.017	6.394	33.446
set2Frame	0.154	0.008	0.161