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CHECK report for NBSplice on malbec1

This page was generated on 2020-04-15 12:14:30 -0400 (Wed, 15 Apr 2020).

Package 1135/1823HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
NBSplice 1.4.0
Gabriela Merino
Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/NBSplice
Branch: RELEASE_3_10
Last Commit: eea7609
Last Changed Date: 2019-10-29 13:11:16 -0400 (Tue, 29 Oct 2019)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: NBSplice
Version: 1.4.0
Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:NBSplice.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings NBSplice_1.4.0.tar.gz
StartedAt: 2020-04-15 05:53:32 -0400 (Wed, 15 Apr 2020)
EndedAt: 2020-04-15 05:54:46 -0400 (Wed, 15 Apr 2020)
EllapsedTime: 73.4 seconds
RetCode: 0
Status:  OK 
CheckDir: NBSplice.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:NBSplice.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings NBSplice_1.4.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/NBSplice.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 ‘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  12.492  1.184   4.418
IsoDataSet-NBTest 12.128  0.940   4.254
IsoDataSet-core   11.696  1.048   3.763
* 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


Installation output

NBSplice.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL NBSplice
###
##############################################################################
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* installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/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)

Tests output

NBSplice.Rcheck/tests/runTests.Rout


R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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 05:54:42 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 
  4.128   0.236   4.406 

Example timings

NBSplice.Rcheck/NBSplice-Ex.timings

nameusersystemelapsed
IsoDataSet-NBTest12.128 0.940 4.254
IsoDataSet-buildLowExpIdx0.7200.1960.374
IsoDataSet-class12.492 1.184 4.418
IsoDataSet-constructor0.2240.1160.228
IsoDataSet-core11.696 1.048 3.763
IsoDataSet-getters0.4600.0280.488
IsoDataSet-initialize0.3000.1160.225
IsoDataSet-print0.2960.0520.244
IsoDataSet-show0.2000.0120.212
NBSpliceRes-GetDSGenes0.0280.0000.026
NBSpliceRes-GetDSResults0.0240.0000.025
NBSpliceRes-GetGeneResults0.0200.0080.030
NBSpliceRes-class0.040.000.04
NBSpliceRes-constructor0.0200.0040.023
NBSpliceRes-getters0.0280.0000.025
NBSpliceRes-initialize0.0200.0000.021
NBSpliceRes-plotGeneResults0.0640.0000.068
NBSpliceRes-plotRatiosDisp0.0320.0040.037
NBSpliceRes-plotVolcano0.0320.0000.033
NBSpliceRes-print0.0320.0000.033
NBSpliceRes-show0.0320.0000.033
totalGeneCounts0.2160.0680.128