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BioC 3.4: CHECK report for transcriptR on morelia

This page was generated on 2017-04-15 16:27:05 -0400 (Sat, 15 Apr 2017).

Package 1246/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
transcriptR 1.2.0
Armen R. Karapetyan
Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/transcriptR
Last Changed Rev: 122710 / Revision: 128728
Last Changed Date: 2016-10-17 14:45:06 -0400 (Mon, 17 Oct 2016)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: transcriptR
Version: 1.2.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings transcriptR_1.2.0.tar.gz
StartedAt: 2017-04-15 08:58:30 -0700 (Sat, 15 Apr 2017)
EndedAt: 2017-04-15 09:04:43 -0700 (Sat, 15 Apr 2017)
EllapsedTime: 373.3 seconds
RetCode: 0
Status:  OK 
CheckDir: transcriptR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings transcriptR_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/transcriptR.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.2.0’
* 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 sizes of PDF files under ‘inst/doc’ ... 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 11.117  0.429  11.601
predictStrand-methods            7.579  0.387   7.971
peaksToBed-methods               6.547  0.355   6.902
* 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-methods0.1070.0170.124
annotateTranscripts-methods2.8660.0942.963
breakTranscriptsByPeaks-methods11.117 0.42911.601
constructCDS0.0020.0080.011
constructTDS0.2490.0280.276
detectTranscripts-methods1.1630.0681.231
estimateBackground-methods0.6770.0390.716
estimateGapDistance-methods0.7780.0490.827
exportCoverage-methods0.2090.0160.225
getConfusionMatrix-methods0.0030.0070.010
getGenomicAnnot-methods0.0040.0070.011
getPeaks-methods0.0250.0070.033
getPredictorSignificance-methods0.0030.0080.011
getProbTreshold-methods0.0030.0080.010
getQuadProb-methods0.2130.0180.231
getTestedGapDistances-methods0.2140.0110.226
getTranscripts-methods0.2190.0080.227
peaksToBed-methods6.5470.3556.902
plotErrorRate-methods1.5330.0871.621
plotFeatures-methods2.9990.0163.020
plotGenomicAnnot-methods0.4640.0100.475
plotROC-methods1.7410.0231.766
predictStrand-methods7.5790.3877.971
predictTssOverlap-methods1.7330.0271.762
show0.2390.0190.257
transcriptsToBed-methods1.4020.0761.479