Package: MetaCyto

Version: 1.4.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings MetaCyto_1.4.0.tar.gz

StartedAt: 2018-04-12 06:05:40 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 06:11:03 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 322.8 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 --no-vignettes --timings MetaCyto_1.4.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/MetaCyto.Rcheck’
* using R version 3.4.4 (2018-03-15)
* 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 ‘1.4.0’
* 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 loading without being on the library search path ... 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
labelCluster        73.058  7.629  82.493
autoCluster.batch   57.374 11.834  71.751
searchCluster.batch 22.760  2.151  25.517
flowSOM.MC          12.963  3.314  16.770
searchCluster        7.419  0.553   8.138
densityPlot          4.421  0.845   5.405
clusterStats         4.255  0.839   5.239
* 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-3.6-bioc/meat/MetaCyto.Rcheck/00check.log’
for details.

* installing *source* package ‘MetaCyto’ ...
** R
** inst
** preparing 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	57.374	11.834	71.751
clusterStats	4.255	0.839	5.239
collectData	0.092	0.001	0.093
densityPlot	4.421	0.845	5.405
fcsInfoParser	0.091	0.001	0.093
filterLabels	0.002	0.001	0.002
findCutoff	1.065	0.251	1.361
flowHC	2.120	0.117	2.272
flowSOM.MC	12.963	3.314	16.770
glmAnalysis	0.495	0.009	0.508
labelCluster	73.058	7.629	82.493
labelSummary	0.491	0.003	0.500
markerFinder	0.024	0.001	0.025
metaAnalysis	0.119	0.003	0.124
nameUpdator	1.290	0.024	1.335
panelSummary	0.036	0.001	0.037
plotGA	1.142	0.005	1.162
preprocessing	0.479	0.008	0.496
preprocessing.batch	1.275	0.019	1.318
sampleInfoParser	0.005	0.000	0.005
searchCluster	7.419	0.553	8.138
searchCluster.batch	22.760	2.151	25.517
set2Frame	0.106	0.010	0.117