Package: MetaCyto

Version: 1.5.1

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_1.5.1.tar.gz

StartedAt: 2019-04-09 02:04:34 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 02:09:48 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 313.7 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_1.5.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/MetaCyto.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* 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 ‘1.5.1’
* 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   67.024 13.405  81.338
labelCluster        59.229 10.958  70.930
searchCluster.batch 16.864  2.874  19.941
flowSOM.MC          14.973  4.424  19.634
searchCluster        5.404  0.698   6.132
densityPlot          5.085  0.628   5.786
clusterStats         4.897  0.488   5.446
* 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.

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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/3.6/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	67.024	13.405	81.338
clusterStats	4.897	0.488	5.446
collectData	0.036	0.002	0.039
densityPlot	5.085	0.628	5.786
fcsInfoParser	0.120	0.002	0.123
filterLabels	0.001	0.000	0.001
findCutoff	1.292	0.181	1.487
flowHC	2.515	0.133	2.672
flowSOM.MC	14.973	4.424	19.634
glmAnalysis	0.412	0.011	0.429
labelCluster	59.229	10.958	70.930
labelSummary	0.540	0.008	0.549
markerFinder	0.020	0.001	0.022
metaAnalysis	0.090	0.003	0.092
nameUpdator	1.231	0.042	1.279
panelSummary	0.026	0.001	0.027
plotGA	0.714	0.007	0.724
preprocessing	0.466	0.003	0.473
preprocessing.batch	1.284	0.017	1.314
sampleInfoParser	0.005	0.001	0.006
searchCluster	5.404	0.698	6.132
searchCluster.batch	16.864	2.874	19.941
set2Frame	0.114	0.005	0.122