Package: SubCellBarCode

Version: 1.0.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:SubCellBarCode.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings SubCellBarCode_1.0.0.tar.gz

StartedAt: 2019-10-16 07:13:40 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 07:17:18 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 217.8 seconds

RetCode: 0

Status:  OK

CheckDir: SubCellBarCode.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:SubCellBarCode.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings SubCellBarCode_1.0.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/SubCellBarCode.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SubCellBarCode/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SubCellBarCode’ version ‘1.0.0’
* package encoding: UTF-8
* 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 ‘SubCellBarCode’ 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 ... OK
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                               user system elapsed
applyThresholdCompartment    23.243  0.658  24.798
computeThresholdCompartment  17.304  0.344  17.649
applyThresholdNeighborhood   15.998  0.527  16.742
computeThresholdNeighborhood 14.725  0.324  15.049
candidateRelocatedProteins   11.979  0.847  12.829
svmClassification            12.000  0.338  12.339
* 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: OK

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL SubCellBarCode
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘SubCellBarCode’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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 (SubCellBarCode)

name	user	system	elapsed
applyThresholdCompartment	23.243	0.658	24.798
applyThresholdNeighborhood	15.998	0.527	16.742
calRowMean	0.009	0.001	0.010
calculateCoveredProtein	0.281	0.003	0.285
candidateRelocatedProteins	11.979	0.847	12.829
computeThresholdCompartment	17.304	0.344	17.649
computeThresholdNeighborhood	14.725	0.324	15.049
hcc827Ctrl	0.006	0.000	0.007
hcc827CtrlPSMCount	0.009	0.000	0.009
hcc827GEF	0.005	0.001	0.006
hcc827GEFClass	0.002	0.000	0.003
hcc827GefPSMCount	0.001	0.000	0.003
loadData	0.002	0.000	0.002
markerQualityControl	0.750	0.009	0.761
mergeCls	0.014	0.001	0.015
mergeProbability	0.011	0.001	0.012
plotBarcode	1.183	0.003	1.187
plotMultipleProtein	0.446	0.002	0.448
replacePrediction	0.009	0.001	0.009
sankeyPlot	0.054	0.003	0.057
sumProbability	0.011	0.001	0.012
svmClassification	12.000	0.338	12.339
tsneVisualization	0.333	0.005	0.339