Package: SubCellBarCode

Version: 1.0.0

Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:SubCellBarCode.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings SubCellBarCode_1.0.0.tar.gz

StartedAt: 2019-10-16 05:19:08 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 05:21:56 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 168.5 seconds

RetCode: 0

Status:  OK

CheckDir: SubCellBarCode.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:SubCellBarCode.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings SubCellBarCode_1.0.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/SubCellBarCode.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 ‘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
applyThresholdNeighborhood   19.617  0.008  19.630
applyThresholdCompartment    17.956  0.064  18.020
computeThresholdCompartment  16.930  0.000  16.935
computeThresholdNeighborhood 15.504  0.008  15.549
svmClassification            14.101  0.008  14.174
candidateRelocatedProteins    7.772  0.000   7.773
* 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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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL SubCellBarCode
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/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	17.956	0.064	18.020
applyThresholdNeighborhood	19.617	0.008	19.630
calRowMean	0.007	0.000	0.008
calculateCoveredProtein	0.226	0.000	0.227
candidateRelocatedProteins	7.772	0.000	7.773
computeThresholdCompartment	16.930	0.000	16.935
computeThresholdNeighborhood	15.504	0.008	15.549
hcc827Ctrl	0.005	0.000	0.005
hcc827CtrlPSMCount	0.009	0.000	0.009
hcc827GEF	0.003	0.000	0.003
hcc827GEFClass	0.002	0.000	0.002
hcc827GefPSMCount	0.001	0.000	0.002
loadData	0.001	0.000	0.001
markerQualityControl	0.694	0.000	0.698
mergeCls	0.005	0.000	0.005
mergeProbability	0.004	0.000	0.004
plotBarcode	0.593	0.000	0.593
plotMultipleProtein	0.458	0.000	0.459
replacePrediction	0.007	0.000	0.007
sankeyPlot	0.048	0.000	0.048
sumProbability	0.008	0.000	0.007
svmClassification	14.101	0.008	14.174
tsneVisualization	0.191	0.000	0.191