Package: MetaCyto

Version: 1.8.0

Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:MetaCyto.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings MetaCyto_1.8.0.tar.gz

StartedAt: 2020-04-15 05:17:24 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 05:23:27 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 363.2 seconds

RetCode: 0

Status:  OK

CheckDir: MetaCyto.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:MetaCyto.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings MetaCyto_1.8.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/MetaCyto.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘1.8.0’
* 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 or elapsed time > 5s
                      user system elapsed
autoCluster.batch   65.812 13.152  79.579
labelCluster        59.020  7.296  92.513
searchCluster.batch 17.012  2.508  20.883
flowSOM.MC          14.856  0.028  16.038
searchCluster        5.840  0.572   6.880
clusterStats         5.388  0.848   6.324
densityPlot          5.200  0.012   5.695
* 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-3.10-bioc/meat/MetaCyto.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL MetaCyto
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* installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/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	65.812	13.152	79.579
clusterStats	5.388	0.848	6.324
collectData	0.04	0.00	0.07
densityPlot	5.200	0.012	5.695
fcsInfoParser	0.104	0.000	0.114
filterLabels	0.004	0.000	0.002
findCutoff	1.064	0.220	1.376
flowHC	2.424	0.036	2.550
flowSOM.MC	14.856	0.028	16.038
glmAnalysis	0.444	0.000	0.481
labelCluster	59.020	7.296	92.513
labelSummary	0.500	0.004	0.520
markerFinder	0.028	0.004	0.044
metaAnalysis	0.132	0.000	0.178
nameUpdator	1.296	0.000	1.353
panelSummary	0.024	0.000	0.024
plotGA	0.668	0.000	0.709
preprocessing	0.592	0.000	0.596
preprocessing.batch	1.560	0.000	2.032
sampleInfoParser	0.004	0.000	0.006
searchCluster	5.840	0.572	6.880
searchCluster.batch	17.012	2.508	20.883
set2Frame	0.116	0.000	0.116