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This page was generated on 2021-12-01 17:17:31 -0500 (Wed, 01 Dec 2021).

CHECK results for NBSplice on nebbiolo2

To the developers/maintainers of the NBSplice package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/NBSplice.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1271/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
NBSplice 1.12.0  (landing page)
Gabriela Merino
Snapshot Date: 2021-11-30 04:15:05 -0500 (Tue, 30 Nov 2021)
git_url: https://git.bioconductor.org/packages/NBSplice
git_branch: RELEASE_3_14
git_last_commit: 9f992af
git_last_commit_date: 2021-10-26 12:45:43 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: NBSplice
Version: 1.12.0
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:NBSplice.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings NBSplice_1.12.0.tar.gz
StartedAt: 2021-11-30 10:07:30 -0500 (Tue, 30 Nov 2021)
EndedAt: 2021-11-30 10:09:12 -0500 (Tue, 30 Nov 2021)
EllapsedTime: 101.7 seconds
RetCode: 0
Status:   OK  
CheckDir: NBSplice.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:NBSplice.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings NBSplice_1.12.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/NBSplice.Rcheck’
* using R version 4.1.2 (2021-11-01)
* 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 ‘1.12.0’
* 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 ‘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 (user + system) or elapsed time > 5s
                            user system elapsed
IsoDataSet-core           29.650  2.528   7.972
IsoDataSet-class          28.170  2.220   8.625
IsoDataSet-NBTest         23.317  1.236   7.286
IsoDataSet-buildLowExpIdx 14.113  0.535   3.811
* 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-3.14-bioc/R/bin/R CMD INSTALL NBSplice
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.14-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 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 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 -- Tue Nov 30 10:09:09 2021 
*********************************************** 
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 
 25.733   0.211  25.926 

Example timings

NBSplice.Rcheck/NBSplice-Ex.timings

nameusersystemelapsed
IsoDataSet-NBTest23.317 1.236 7.286
IsoDataSet-buildLowExpIdx14.113 0.535 3.811
IsoDataSet-class28.170 2.220 8.625
IsoDataSet-constructor0.0510.0430.834
IsoDataSet-core29.650 2.528 7.972
IsoDataSet-getters0.3770.0160.392
IsoDataSet-initialize1.9690.4200.984
IsoDataSet-print0.1960.0560.252
IsoDataSet-show0.1440.0870.230
NBSpliceRes-GetDSGenes0.0160.0000.016
NBSpliceRes-GetDSResults0.0150.0000.015
NBSpliceRes-GetGeneResults0.0170.0000.017
NBSpliceRes-class0.0180.0040.022
NBSpliceRes-constructor0.0140.0000.014
NBSpliceRes-getters0.0120.0040.015
NBSpliceRes-initialize0.0140.0000.013
NBSpliceRes-plotGeneResults0.0410.0040.045
NBSpliceRes-plotRatiosDisp0.0210.0030.024
NBSpliceRes-plotVolcano0.0220.0010.023
NBSpliceRes-print0.0190.0040.022
NBSpliceRes-show0.0210.0000.021
totalGeneCounts2.0300.5330.971