Package: ASpli

Version: 1.10.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ASpli.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ASpli_1.10.0.tar.gz

StartedAt: 2019-10-16 00:38:26 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 00:47:16 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 529.8 seconds

RetCode: 0

Status:  OK

CheckDir: ASpli.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:ASpli.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ASpli_1.10.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/ASpli.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 ‘ASpli/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ASpli’ version ‘1.10.0’
* 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 ‘ASpli’ 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                             user system elapsed
plotGenomicRegions         23.182  0.298  23.483
plotBins                   13.468  0.195  13.662
ASpli-package              12.627  0.595  13.325
mergeBinDUAS-method        10.648  0.121  10.801
AsDiscover-methods          8.449  0.187   8.690
subset-methods              7.834  0.033   7.868
DUreport                    7.279  0.171   7.549
junctionDUreport            7.062  0.040   7.102
containsJunctions-function  6.793  0.043   6.836
filterDU-method             6.594  0.044   6.639
rds                         6.565  0.067   6.631
DUreportBinSplice-method    6.542  0.047   6.591
readCounts                  6.010  0.042   6.054
* 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 ASpli
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘ASpli’ ...
** using staged installation
** 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 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 (ASpli)

name	user	system	elapsed
ASpli-package	12.627	0.595	13.325
AsDiscover-methods	8.449	0.187	8.690
DUreport	7.279	0.171	7.549
DUreportBinSplice-method	6.542	0.047	6.591
acc_AS	0.031	0.004	0.038
acc_DU	0.014	0.002	0.018
acc_counts	0.028	0.004	0.034
acc_features	0.304	0.001	0.305
binGenome	3.953	0.021	3.973
containsJunctions-function	6.793	0.043	6.836
example_data	0.776	0.022	0.803
filterDU-method	6.594	0.044	6.639
getConditions-function	0.011	0.001	0.012
junctionDUreport	7.062	0.040	7.102
loadBAM	0.148	0.004	0.152
mergeBinDUAS-method	10.648	0.121	10.801
plotBins	13.468	0.195	13.662
plotGenomicRegions	23.182	0.298	23.483
rds	6.565	0.067	6.631
readCounts	6.010	0.042	6.054
subset-methods	7.834	0.033	7.868