Package: NBSplice

Version: 1.4.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:NBSplice.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings NBSplice_1.4.0.tar.gz

StartedAt: 2020-04-15 04:11:56 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 04:13:34 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 97.5 seconds

RetCode: 0

Status:  OK

CheckDir: NBSplice.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:NBSplice.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings NBSplice_1.4.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/NBSplice.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 ‘NBSplice/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘NBSplice’ version ‘1.4.0’
* 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 ‘NBSplice’ 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
IsoDataSet-class  15.572  2.389   5.440
IsoDataSet-core   15.150  2.262   4.963
IsoDataSet-NBTest 14.882  2.012   5.168
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 OK
* 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 NBSplice
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘NBSplice’ ...
** using staged installation
** R
** data
** 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 (NBSplice)

R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> BiocGenerics:::testPackage("NBSplice")
Loading required package: BiocParallel
Loading required package: ggplot2


RUNIT TEST PROTOCOL -- Wed Apr 15 04:13:22 2020 
*********************************************** 
Number of test functions: 20 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
NBSplice RUnit Tests - 20 test functions, 0 errors, 0 failures
Number of test functions: 20 
Number of errors: 0 
Number of failures: 0 
> 
> 
> proc.time()
   user  system elapsed 
  4.868   0.467   5.384 

name	user	system	elapsed
IsoDataSet-NBTest	14.882	2.012	5.168
IsoDataSet-buildLowExpIdx	1.133	0.496	0.515
IsoDataSet-class	15.572	2.389	5.440
IsoDataSet-constructor	0.421	0.368	0.323
IsoDataSet-core	15.150	2.262	4.963
IsoDataSet-getters	0.319	0.055	0.374
IsoDataSet-initialize	0.437	0.361	0.307
IsoDataSet-print	0.224	0.061	0.286
IsoDataSet-show	0.167	0.027	0.196
NBSpliceRes-GetDSGenes	0.020	0.007	0.027
NBSpliceRes-GetDSResults	0.017	0.008	0.025
NBSpliceRes-GetGeneResults	0.026	0.007	0.033
NBSpliceRes-class	0.037	0.009	0.048
NBSpliceRes-constructor	0.018	0.008	0.026
NBSpliceRes-getters	0.026	0.009	0.035
NBSpliceRes-initialize	0.017	0.008	0.025
NBSpliceRes-plotGeneResults	0.071	0.013	0.107
NBSpliceRes-plotRatiosDisp	0.038	0.010	0.064
NBSpliceRes-plotVolcano	0.036	0.010	0.048
NBSpliceRes-print	0.035	0.012	0.047
NBSpliceRes-show	0.036	0.011	0.046
totalGeneCounts	0.238	0.268	0.288