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This page was generated on 2021-10-15 15:05:46 -0400 (Fri, 15 Oct 2021).

CHECK results for NBSplice on nebbiolo1

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 1250/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
NBSplice 1.10.0  (landing page)
Gabriela Merino
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/NBSplice
git_branch: RELEASE_3_13
git_last_commit: 58b6cb9
git_last_commit_date: 2021-05-19 12:36:47 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 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: 1.10.0
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:NBSplice.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings NBSplice_1.10.0.tar.gz
StartedAt: 2021-10-14 10:46:47 -0400 (Thu, 14 Oct 2021)
EndedAt: 2021-10-14 10:48:28 -0400 (Thu, 14 Oct 2021)
EllapsedTime: 101.0 seconds
RetCode: 0
Status:   OK  
CheckDir: NBSplice.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:NBSplice.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings NBSplice_1.10.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/NBSplice.Rcheck’
* using R version 4.1.1 (2021-08-10)
* 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 ‘1.10.0’
* 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 ‘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-class          25.446  2.565   7.461
IsoDataSet-core           24.224  2.393   7.114
IsoDataSet-NBTest         20.802  1.669   6.513
IsoDataSet-buildLowExpIdx 11.361  0.453   4.197
* 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-3.13-bioc/R/bin/R CMD INSTALL NBSplice
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.13-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 4.1.1 (2021-08-10) -- "Kick Things"
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 -- Thu Oct 14 10:48:25 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 
 23.874   0.160  24.014 

Example timings

NBSplice.Rcheck/NBSplice-Ex.timings

nameusersystemelapsed
IsoDataSet-NBTest20.802 1.669 6.513
IsoDataSet-buildLowExpIdx11.361 0.453 4.197
IsoDataSet-class25.446 2.565 7.461
IsoDataSet-constructor1.8270.4670.944
IsoDataSet-core24.224 2.393 7.114
IsoDataSet-getters0.3530.0120.366
IsoDataSet-initialize1.7900.4570.884
IsoDataSet-print0.7930.1490.120
IsoDataSet-show0.1020.0000.102
NBSpliceRes-GetDSGenes0.0150.0080.022
NBSpliceRes-GetDSResults0.0150.0000.015
NBSpliceRes-GetGeneResults0.0140.0040.018
NBSpliceRes-class0.0270.0000.027
NBSpliceRes-constructor0.0140.0000.014
NBSpliceRes-getters0.0160.0000.016
NBSpliceRes-initialize0.0130.0000.013
NBSpliceRes-plotGeneResults0.0370.0040.040
NBSpliceRes-plotRatiosDisp0.0180.0040.022
NBSpliceRes-plotVolcano0.020.000.02
NBSpliceRes-print0.0190.0000.019
NBSpliceRes-show0.0190.0000.019
totalGeneCounts0.0170.0330.692