Package: ASpli

Version: 1.12.0

Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:ASpli.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings ASpli_1.12.0.tar.gz

StartedAt: 2020-04-15 04:01:30 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 04:09:12 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 462.0 seconds

RetCode: 0

Status:  OK

CheckDir: ASpli.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:ASpli.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings ASpli_1.12.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/ASpli.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-pc-linux-gnu (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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                             user system elapsed
plotGenomicRegions         16.248  0.036  16.341
plotBins                   12.384  0.020  12.438
ASpli-package              11.608  0.124  11.816
mergeBinDUAS-method        11.372  0.008  11.397
AsDiscover-methods          8.408  0.016   8.491
DUreportBinSplice-method    6.980  0.012   7.004
junctionDUreport            6.868  0.012   6.897
DUreport                    6.380  0.020   6.416
containsJunctions-function  6.228  0.012   6.256
filterDU-method             6.200  0.008   6.217
subset-methods              5.492  0.008   5.511
readCounts                  5.232  0.012   5.267
rds                         4.980  0.016   5.011
* 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-3.10-bioc/R/bin/R CMD INSTALL ASpli
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* installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/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	11.608	0.124	11.816
AsDiscover-methods	8.408	0.016	8.491
DUreport	6.380	0.020	6.416
DUreportBinSplice-method	6.980	0.012	7.004
acc_AS	0.024	0.004	0.321
acc_DU	0.012	0.000	0.138
acc_counts	0.016	0.004	0.212
acc_features	0.380	0.000	0.381
binGenome	3.032	0.004	3.038
containsJunctions-function	6.228	0.012	6.256
example_data	0.768	0.000	0.791
filterDU-method	6.200	0.008	6.217
getConditions-function	0.004	0.000	0.005
junctionDUreport	6.868	0.012	6.897
loadBAM	0.212	0.004	0.221
mergeBinDUAS-method	11.372	0.008	11.397
plotBins	12.384	0.020	12.438
plotGenomicRegions	16.248	0.036	16.341
rds	4.980	0.016	5.011
readCounts	5.232	0.012	5.267
subset-methods	5.492	0.008	5.511