Package: ASpli

Version: 1.13.0

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_1.13.0.tar.gz

StartedAt: 2020-01-16 01:50:25 -0500 (Thu, 16 Jan 2020)

EndedAt: 2020-01-16 02:01:55 -0500 (Thu, 16 Jan 2020)

EllapsedTime: 689.5 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_1.13.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/ASpli.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 ‘ASpli/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ASpli’ version ‘1.13.0’
* 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 (user + system) or elapsed time > 5s
                             user system elapsed
plotGenomicRegions         32.833  0.500  39.272
plotBins                   22.011  0.397  25.841
mergeBinDUAS-method        17.655  0.187  17.853
ASpli-package              16.975  0.818  17.910
subset-methods             12.603  0.044  12.658
AsDiscover-methods         12.485  0.135  12.626
junctionDUreport           10.278  0.038  10.318
containsJunctions-function 10.116  0.055  10.179
readCounts                 10.067  0.050  10.142
DUreportBinSplice-method    9.762  0.051   9.816
filterDU-method             9.564  0.042   9.608
rds                         9.453  0.042   9.503
DUreport                    9.158  0.043   9.215
binGenome                   5.554  0.022   5.576
* 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/4.0/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	16.975	0.818	17.910
AsDiscover-methods	12.485	0.135	12.626
DUreport	9.158	0.043	9.215
DUreportBinSplice-method	9.762	0.051	9.816
acc_AS	0.035	0.005	0.044
acc_DU	0.013	0.002	0.016
acc_counts	0.030	0.004	0.035
acc_features	0.515	0.001	0.516
binGenome	5.554	0.022	5.576
containsJunctions-function	10.116	0.055	10.179
example_data	1.170	0.021	1.205
filterDU-method	9.564	0.042	9.608
getConditions-function	0.013	0.001	0.014
junctionDUreport	10.278	0.038	10.318
loadBAM	0.276	0.006	0.281
mergeBinDUAS-method	17.655	0.187	17.853
plotBins	22.011	0.397	25.841
plotGenomicRegions	32.833	0.500	39.272
rds	9.453	0.042	9.503
readCounts	10.067	0.050	10.142
subset-methods	12.603	0.044	12.658