Package: ASpli

Version: 1.10.0

Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:ASpli.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings ASpli_1.10.0.tar.gz

StartedAt: 2019-10-15 23:51:19 -0400 (Tue, 15 Oct 2019)

EndedAt: 2019-10-15 23:57:41 -0400 (Tue, 15 Oct 2019)

EllapsedTime: 382.0 seconds

RetCode: 0

Status:  OK

CheckDir: ASpli.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:ASpli.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings ASpli_1.10.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/ASpli.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 ‘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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                             user system elapsed
plotGenomicRegions         17.087  0.047  17.209
plotBins                    9.217  0.007   9.261
ASpli-package               8.933  0.200   9.181
mergeBinDUAS-method         8.801  0.008   8.843
subset-methods              6.232  0.012   6.289
junctionDUreport            5.707  0.004   5.753
containsJunctions-function  5.589  0.001   5.605
rds                         5.318  0.005   5.322
readCounts                  5.243  0.004   5.258
filterDU-method             5.153  0.004   5.171
AsDiscover-methods          5.088  0.012   5.108
* 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 ASpli
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* installing to library ‘/home/biocbuild/bbs-3.9-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	8.933	0.200	9.181
AsDiscover-methods	5.088	0.012	5.108
DUreport	4.599	0.008	4.613
DUreportBinSplice-method	4.581	0.000	4.604
acc_AS	0.023	0.004	0.060
acc_DU	0.009	0.000	0.019
acc_counts	0.021	0.000	0.030
acc_features	0.245	0.000	0.246
binGenome	2.803	0.000	2.806
containsJunctions-function	5.589	0.001	5.605
example_data	0.603	0.009	0.633
filterDU-method	5.153	0.004	5.171
getConditions-function	0.007	0.000	0.008
junctionDUreport	5.707	0.004	5.753
loadBAM	0.182	0.008	0.191
mergeBinDUAS-method	8.801	0.008	8.843
plotBins	9.217	0.007	9.261
plotGenomicRegions	17.087	0.047	17.209
rds	5.318	0.005	5.322
readCounts	5.243	0.004	5.258
subset-methods	6.232	0.012	6.289