Package: NBSplice

Version: 1.1.7

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_1.1.7.tar.gz

StartedAt: 2019-04-09 02:29:01 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 02:30:23 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 82.6 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: NBSplice.Rcheck

Warnings: 1

##############################################################################
##############################################################################
###
### Running 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_1.1.7.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/NBSplice.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* 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 ‘1.1.7’
* 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 ... WARNING
Found the following files with non-portable file names:
  vignettes/NBSplice-vignette_cache/html/expMat built_bb534d843cf91b501cc117752c01b5a1.RData
  vignettes/NBSplice-vignette_cache/html/expMat built_bb534d843cf91b501cc117752c01b5a1.rdb
  vignettes/NBSplice-vignette_cache/html/expMat built_bb534d843cf91b501cc117752c01b5a1.rdx
  vignettes/NBSplice-vignette_cache/html/object loading2_5158601cc5ca397804e3c1fa1f41b30f.RData
  vignettes/NBSplice-vignette_cache/html/object loading2_5158601cc5ca397804e3c1fa1f41b30f.rdb
  vignettes/NBSplice-vignette_cache/html/object loading2_5158601cc5ca397804e3c1fa1f41b30f.rdx
These are not fully portable file names.
See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
Found the following non-portable file path:
  NBSplice/vignettes/NBSplice-vignette_cache/html/object loading2_5158601cc5ca397804e3c1fa1f41b30f.RData

Tarballs are only required to store paths of up to 100 bytes and cannot
store those of more than 256 bytes, with restrictions including to 100
bytes for the final component.
See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
* 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  16.104  2.822   5.918
IsoDataSet-NBTest 15.502  2.255   5.454
IsoDataSet-core   15.308  2.178   5.236
* 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: 1 WARNING
See
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/NBSplice.Rcheck/00check.log’
for details.

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘NBSplice’ ...
** 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
* DONE (NBSplice)

R Under development (unstable) (2018-11-27 r75683) -- "Unsuffered Consequences"
Copyright (C) 2018 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 -- Tue Apr  9 02:30:17 2019 
*********************************************** 
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 
  4.432   0.365   4.797 

name	user	system	elapsed
IsoDataSet-NBTest	15.502	2.255	5.454
IsoDataSet-buildLowExpIdx	1.098	0.498	0.759
IsoDataSet-class	16.104	2.822	5.918
IsoDataSet-constructor	0.464	0.300	0.304
IsoDataSet-core	15.308	2.178	5.236
IsoDataSet-getters	0.412	0.037	0.451
IsoDataSet-initialize	0.479	0.338	0.334
IsoDataSet-print	0.213	0.038	0.251
IsoDataSet-show	0.207	0.021	0.230
NBSpliceRes-GetDSGenes	0.023	0.004	0.027
NBSpliceRes-GetDSResults	0.015	0.002	0.018
NBSpliceRes-GetGeneResults	0.019	0.003	0.021
NBSpliceRes-class	0.026	0.004	0.031
NBSpliceRes-constructor	0.014	0.002	0.016
NBSpliceRes-getters	0.016	0.002	0.018
NBSpliceRes-initialize	0.016	0.003	0.019
NBSpliceRes-plotGeneResults	0.075	0.006	0.081
NBSpliceRes-plotRatiosDisp	0.042	0.004	0.046
NBSpliceRes-plotVolcano	0.035	0.003	0.038
NBSpliceRes-print	0.030	0.003	0.034
NBSpliceRes-show	0.030	0.003	0.034
totalGeneCounts	0.074	0.047	0.245