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CHECK report for transcriptR on merida2

This page was generated on 2018-10-17 08:55:43 -0400 (Wed, 17 Oct 2018).

Package 1498/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
transcriptR 1.8.0
Armen R. Karapetyan
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/transcriptR
Branch: RELEASE_3_7
Last Commit: 622502e
Last Changed Date: 2018-04-30 10:35:39 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: transcriptR
Version: 1.8.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:transcriptR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings transcriptR_1.8.0.tar.gz
StartedAt: 2018-10-17 00:28:56 -0400 (Wed, 17 Oct 2018)
EndedAt: 2018-10-17 00:36:20 -0400 (Wed, 17 Oct 2018)
EllapsedTime: 443.9 seconds
RetCode: 0
Status:  OK 
CheckDir: transcriptR.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:transcriptR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings transcriptR_1.8.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/transcriptR.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘transcriptR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘transcriptR’ version ‘1.8.0’
* 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 ‘transcriptR’ 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 ... NOTE
  Error in .requirePackage(package) : 
    unable to find required package 'transcriptR'
  Calls: <Anonymous> ... getClass -> getClassDef -> .classEnv -> .requirePackage
  Execution halted
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                                 user system elapsed
breakTranscriptsByPeaks-methods 9.575  0.361  10.884
peaksToBed-methods              7.460  0.242   9.050
predictStrand-methods           6.072  0.225   6.597
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.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 NOTE
See
  ‘/Users/biocbuild/bbs-3.7-bioc/meat/transcriptR.Rcheck/00check.log’
for details.



Installation output

transcriptR.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘transcriptR’ ...
** 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 (transcriptR)

Tests output

transcriptR.Rcheck/tests/testthat.Rout


R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
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.

> library(testthat)
> library(transcriptR)
> 
> test_check("transcriptR")
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 87 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 77.314   2.623  80.423 

Example timings

transcriptR.Rcheck/transcriptR-Ex.timings

nameusersystemelapsed
addFeature-methods0.1210.0030.128
annotateTranscripts-methods3.5620.1143.697
breakTranscriptsByPeaks-methods 9.575 0.36110.884
constructCDS0.0060.0020.008
constructTDS0.3790.0360.672
detectTranscripts-methods1.5210.0961.894
estimateBackground-methods0.5050.0550.570
estimateGapDistance-methods1.9590.0552.028
exportCoverage-methods0.2840.0210.309
getConfusionMatrix-methods0.0060.0010.006
getGenomicAnnot-methods0.0050.0010.005
getPeaks-methods0.0340.0020.036
getPredictorSignificance-methods0.0040.0010.006
getProbTreshold-methods0.0040.0010.005
getQuadProb-methods0.2960.0150.312
getTestedGapDistances-methods0.3260.0180.348
getTranscripts-methods0.2830.0100.294
peaksToBed-methods7.4600.2429.050
plotErrorRate-methods1.0980.0611.169
plotFeatures-methods3.0490.0223.104
plotGenomicAnnot-methods0.5540.0040.559
plotROC-methods2.3310.0313.497
predictStrand-methods6.0720.2256.597
predictTssOverlap-methods2.0260.0282.097
show0.3590.0250.623
transcriptsToBed-methods1.8000.0972.838