Package: ASpli

Version: 1.12.0

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_1.12.0.tar.gz

StartedAt: 2020-04-15 00:29:26 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 00:37:04 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 458.1 seconds

RetCode: 0

Status:  OK

CheckDir: ASpli.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running 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_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/ASpli.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘1.12.0’
* 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         21.069  0.156  21.469
plotBins                   14.178  0.045  14.366
ASpli-package              11.276  0.292  11.693
mergeBinDUAS-method        11.093  0.097  11.303
AsDiscover-methods          8.490  0.042   8.637
subset-methods              7.836  0.023   7.954
junctionDUreport            6.733  0.021   6.804
readCounts                  6.439  0.065   6.566
containsJunctions-function  6.442  0.023   6.501
rds                         6.425  0.024   6.534
DUreportBinSplice-method    6.399  0.022   6.466
DUreport                    6.226  0.024   6.312
filterDU-method             6.114  0.022   6.169
* 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

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL ASpli
###
##############################################################################
##############################################################################


* 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	11.276	0.292	11.693
AsDiscover-methods	8.490	0.042	8.637
DUreport	6.226	0.024	6.312
DUreportBinSplice-method	6.399	0.022	6.466
acc_AS	0.022	0.002	0.024
acc_DU	0.008	0.001	0.009
acc_counts	0.017	0.001	0.020
acc_features	0.306	0.001	0.308
binGenome	3.168	0.013	3.208
containsJunctions-function	6.442	0.023	6.501
example_data	0.762	0.011	0.790
filterDU-method	6.114	0.022	6.169
getConditions-function	0.010	0.001	0.010
junctionDUreport	6.733	0.021	6.804
loadBAM	0.177	0.003	0.184
mergeBinDUAS-method	11.093	0.097	11.303
plotBins	14.178	0.045	14.366
plotGenomicRegions	21.069	0.156	21.469
rds	6.425	0.024	6.534
readCounts	6.439	0.065	6.566
subset-methods	7.836	0.023	7.954