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This page was generated on 2021-11-27 14:05:47 -0500 (Sat, 27 Nov 2021).

CHECK results for NBSplice on merida1

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 1260/2068HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
NBSplice 1.13.0  (landing page)
Gabriela Merino
Snapshot Date: 2021-11-26 14:50:14 -0500 (Fri, 26 Nov 2021)
git_url: https://git.bioconductor.org/packages/NBSplice
git_branch: master
git_last_commit: 363ec28
git_last_commit_date: 2021-10-26 12:45:44 -0500 (Tue, 26 Oct 2021)
nebbiolo1Linux (Ubuntu 20.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    ERROR    OK  
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: NBSplice
Version: 1.13.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:NBSplice.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings NBSplice_1.13.0.tar.gz
StartedAt: 2021-11-27 05:36:21 -0500 (Sat, 27 Nov 2021)
EndedAt: 2021-11-27 05:39:23 -0500 (Sat, 27 Nov 2021)
EllapsedTime: 182.2 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: NBSplice.Rcheck
Warnings: 1

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:NBSplice.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings NBSplice_1.13.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/NBSplice.Rcheck’
* using R Under development (unstable) (2021-11-01 r81125)
* using platform: x86_64-apple-darwin17.0 (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 ‘1.13.0’
* 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 ... WARNING
Found the following files with non-portable file names:
  vignettes/NBSplice-vignette_cache/html/expMat built_0852b59f33c696da513d2457d7e37e3d.RData
  vignettes/NBSplice-vignette_cache/html/expMat built_0852b59f33c696da513d2457d7e37e3d.rdb
  vignettes/NBSplice-vignette_cache/html/expMat built_0852b59f33c696da513d2457d7e37e3d.rdx
  vignettes/NBSplice-vignette_cache/html/object loading2_1e2c84b7bfe4259e22201c99aac6bdf5.RData
  vignettes/NBSplice-vignette_cache/html/object loading2_1e2c84b7bfe4259e22201c99aac6bdf5.rdb
  vignettes/NBSplice-vignette_cache/html/object loading2_1e2c84b7bfe4259e22201c99aac6bdf5.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_1e2c84b7bfe4259e22201c99aac6bdf5.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 (user + system) or elapsed time > 5s
                            user system elapsed
IsoDataSet-class          44.602  4.631  12.922
IsoDataSet-core           40.598  3.692  11.931
IsoDataSet-NBTest         39.074  2.970  11.459
IsoDataSet-buildLowExpIdx 22.865  1.223   6.371
IsoDataSet-constructor     4.645  1.266   1.625
IsoDataSet-initialize      4.237  1.182   1.441
* 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-3.15-bioc/meat/NBSplice.Rcheck/00check.log’
for details.



Installation output

NBSplice.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/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)

Tests output

NBSplice.Rcheck/tests/runTests.Rout


R Under development (unstable) (2021-11-01 r81125) -- "Unsuffered Consequences"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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 -- Sat Nov 27 05:39:12 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 
 48.316   0.426  48.804 

Example timings

NBSplice.Rcheck/NBSplice-Ex.timings

nameusersystemelapsed
IsoDataSet-NBTest39.074 2.97011.459
IsoDataSet-buildLowExpIdx22.865 1.223 6.371
IsoDataSet-class44.602 4.63112.922
IsoDataSet-constructor4.6451.2661.625
IsoDataSet-core40.598 3.69211.931
IsoDataSet-getters0.5060.0340.540
IsoDataSet-initialize4.2371.1821.441
IsoDataSet-print0.2580.0400.299
IsoDataSet-show0.2490.0220.272
NBSpliceRes-GetDSGenes0.0230.0010.025
NBSpliceRes-GetDSResults0.0220.0020.024
NBSpliceRes-GetGeneResults0.0270.0020.029
NBSpliceRes-class0.0320.0020.034
NBSpliceRes-constructor0.0230.0020.024
NBSpliceRes-getters0.0220.0010.023
NBSpliceRes-initialize0.0200.0010.020
NBSpliceRes-plotGeneResults0.0650.0030.069
NBSpliceRes-plotRatiosDisp0.0310.0010.033
NBSpliceRes-plotVolcano0.0320.0010.034
NBSpliceRes-print0.0290.0010.031
NBSpliceRes-show0.0290.0020.031
totalGeneCounts2.2520.5791.464