Back to the "Multiple platform build/check report" A  B  C  D  E  F  G  H  I  J  K  L  M  N  O  P  Q  R  S [T] U  V  W  X  Y  Z 

BioC 3.5: CHECK report for transcriptR on malbec2

This page was generated on 2017-08-16 13:17:08 -0400 (Wed, 16 Aug 2017).

Package 1328/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
transcriptR 1.4.0
Armen R. Karapetyan
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/transcriptR
Last Changed Rev: 129126 / Revision: 131943
Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: transcriptR
Version: 1.4.0
Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings transcriptR_1.4.0.tar.gz
StartedAt: 2017-08-16 02:43:32 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 02:48:57 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 325.4 seconds
RetCode: 0
Status:  OK 
CheckDir: transcriptR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings transcriptR_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/transcriptR.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-pc-linux-gnu (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 ‘1.4.0’
* 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 ‘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 loading without being on the library search path ... 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                                  user system elapsed
breakTranscriptsByPeaks-methods 10.664  0.044  10.741
peaksToBed-methods               7.332  0.008   7.345
predictStrand-methods            5.820  0.040   5.866
* 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: OK

transcriptR.Rcheck/00install.out:

* installing *source* package ‘transcriptR’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (transcriptR)

transcriptR.Rcheck/transcriptR-Ex.timings:

nameusersystemelapsed
addFeature-methods0.2520.0000.251
annotateTranscripts-methods3.5520.0283.582
breakTranscriptsByPeaks-methods10.664 0.04410.741
constructCDS0.0000.0000.003
constructTDS0.2240.0080.234
detectTranscripts-methods1.7360.0081.744
estimateBackground-methods0.4320.0000.430
estimateGapDistance-methods0.9120.0040.919
exportCoverage-methods0.2280.0000.231
getConfusionMatrix-methods0.0000.0000.003
getGenomicAnnot-methods0.0040.0000.004
getPeaks-methods0.0280.0000.029
getPredictorSignificance-methods0.0040.0000.003
getProbTreshold-methods0.0040.0000.004
getQuadProb-methods0.2240.0040.227
getTestedGapDistances-methods0.2160.0040.222
getTranscripts-methods0.2280.0040.232
peaksToBed-methods7.3320.0087.345
plotErrorRate-methods2.1560.0082.442
plotFeatures-methods3.9360.0003.939
plotGenomicAnnot-methods1.2040.0001.205
plotROC-methods1.3120.0041.318
predictStrand-methods5.8200.0405.866
predictTssOverlap-methods1.3400.0001.342
show0.2240.0000.223
transcriptsToBed-methods1.0960.0041.098