Package: MetaCyto

Version: 1.6.0

Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:MetaCyto.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings MetaCyto_1.6.0.tar.gz

StartedAt: 2019-10-16 03:00:25 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 03:04:56 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 271.1 seconds

RetCode: 0

Status:  OK

CheckDir: MetaCyto.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:MetaCyto.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings MetaCyto_1.6.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/MetaCyto.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.6.0’
* 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   64.307 11.313  75.835
labelCluster        51.742  1.445  53.189
searchCluster.batch 16.980  0.360  17.348
flowSOM.MC          11.390  0.052  11.519
searchCluster        5.835  0.360   6.195
densityPlot          4.784  1.072   5.857
* 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-3.9-bioc/meat/MetaCyto.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL MetaCyto
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* installing to library ‘/home/biocbuild/bbs-3.9-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	64.307	11.313	75.835
clusterStats	4.328	0.284	4.620
collectData	0.026	0.000	0.039
densityPlot	4.784	1.072	5.857
fcsInfoParser	0.123	0.000	0.184
filterLabels	0.001	0.000	0.002
findCutoff	1.162	0.328	1.490
flowHC	2.332	0.028	2.360
flowSOM.MC	11.390	0.052	11.519
glmAnalysis	0.421	0.004	0.438
labelCluster	51.742	1.445	53.189
labelSummary	0.301	0.000	0.301
markerFinder	0.021	0.000	0.021
metaAnalysis	0.085	0.000	0.085
nameUpdator	1.044	0.008	1.053
panelSummary	0.017	0.000	0.025
plotGA	0.472	0.004	0.476
preprocessing	0.459	0.000	0.459
preprocessing.batch	1.029	0.000	1.029
sampleInfoParser	0.003	0.000	0.003
searchCluster	5.835	0.360	6.195
searchCluster.batch	16.980	0.360	17.348
set2Frame	0.076	0.000	0.076