Package: SubCellBarCode

Version: 1.3.0

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_1.3.0.tar.gz

StartedAt: 2019-12-20 08:30:00 -0500 (Fri, 20 Dec 2019)

EndedAt: 2019-12-20 08:33:47 -0500 (Fri, 20 Dec 2019)

EllapsedTime: 226.8 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_1.3.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/SubCellBarCode.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* 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 ‘1.3.0’
* 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 (user + system) or elapsed time > 5s
                               user system elapsed
applyThresholdCompartment    25.672  0.832  27.157
computeThresholdCompartment  18.248  0.552  18.801
applyThresholdNeighborhood   16.779  0.710  17.854
computeThresholdNeighborhood 13.884  0.483  14.368
candidateRelocatedProteins   12.243  0.817  13.061
svmClassification            11.489  0.483  11.975
* 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/4.0/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	25.672	0.832	27.157
applyThresholdNeighborhood	16.779	0.710	17.854
calRowMean	0.006	0.001	0.009
calculateCoveredProtein	0.238	0.005	0.244
candidateRelocatedProteins	12.243	0.817	13.061
computeThresholdCompartment	18.248	0.552	18.801
computeThresholdNeighborhood	13.884	0.483	14.368
hcc827Ctrl	0.005	0.001	0.005
hcc827CtrlPSMCount	0.010	0.001	0.011
hcc827GEF	0.006	0.001	0.007
hcc827GEFClass	0.003	0.001	0.004
hcc827GefPSMCount	0.002	0.000	0.002
loadData	0.002	0.000	0.002
markerQualityControl	0.840	0.010	0.852
mergeCls	0.008	0.001	0.008
mergeProbability	0.007	0.001	0.008
plotBarcode	1.153	0.003	1.155
plotMultipleProtein	0.414	0.006	0.420
replacePrediction	0.009	0.001	0.009
sankeyPlot	0.062	0.003	0.064
sumProbability	0.012	0.000	0.013
svmClassification	11.489	0.483	11.975
tsneVisualization	0.351	0.006	0.362