Package: MetaCyto

Version: 1.4.1

Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:MetaCyto.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings MetaCyto_1.4.1.tar.gz

StartedAt: 2019-04-16 01:16:04 -0400 (Tue, 16 Apr 2019)

EndedAt: 2019-04-16 01:20:40 -0400 (Tue, 16 Apr 2019)

EllapsedTime: 276.4 seconds

RetCode: 0

Status:  OK

CheckDir: MetaCyto.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:MetaCyto.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings MetaCyto_1.4.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/MetaCyto.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘1.4.1’
* 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   64.468  9.304  74.039
labelCluster        54.160  3.268  57.559
searchCluster.batch 17.744  2.688  20.509
flowSOM.MC          15.096  0.036  15.163
searchCluster        5.816  0.964   6.810
densityPlot          5.292  0.896   6.210
clusterStats         5.044  0.652   5.719
* 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-3.8-bioc/meat/MetaCyto.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL MetaCyto
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* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/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	64.468	9.304	74.039
clusterStats	5.044	0.652	5.719
collectData	0.052	0.008	0.065
densityPlot	5.292	0.896	6.210
fcsInfoParser	0.116	0.000	0.137
filterLabels	0.004	0.000	0.001
findCutoff	0.944	0.000	0.946
flowHC	2.276	0.020	2.297
flowSOM.MC	15.096	0.036	15.163
glmAnalysis	0.476	0.000	0.478
labelCluster	54.160	3.268	57.559
labelSummary	0.616	0.000	0.620
markerFinder	0.036	0.000	0.034
metaAnalysis	0.132	0.000	0.132
nameUpdator	1.624	0.000	1.624
panelSummary	0.024	0.004	0.065
plotGA	0.712	0.004	0.718
preprocessing	0.676	0.000	0.677
preprocessing.batch	1.608	0.000	1.610
sampleInfoParser	0.004	0.000	0.005
searchCluster	5.816	0.964	6.810
searchCluster.batch	17.744	2.688	20.509
set2Frame	0.116	0.000	0.115