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BioC 3.4: CHECK report for transcriptR on morelia

This page was generated on 2016-09-21 03:55:04 -0700 (Wed, 21 Sep 2016).

Package 1211/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
transcriptR 1.1.2
Armen R. Karapetyan
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/transcriptR
Last Changed Rev: 117512 / Revision: 121152
Last Changed Date: 2016-05-15 13:14:22 -0700 (Sun, 15 May 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / 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: 1.1.2
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings transcriptR_1.1.2.tar.gz
StartedAt: 2016-09-20 14:00:24 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 14:05:14 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 290.6 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_1.1.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/transcriptR.Rcheck’
* using R version 3.3.1 (2016-06-21)
* 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 ‘1.1.2’
* 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 9.383  0.351   9.773
predictStrand-methods           6.347  0.358   6.707
peaksToBed-methods              5.803  0.264   6.067
plotFeatures-methods            1.899  0.013   5.985
* 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-methods0.0960.0060.102
annotateTranscripts-methods2.9600.0903.052
breakTranscriptsByPeaks-methods9.3830.3519.773
constructCDS0.0030.0070.010
constructTDS0.2480.0180.265
detectTranscripts-methods1.4850.0911.576
estimateBackground-methods0.3360.0340.370
estimateGapDistance-methods1.2580.0481.306
exportCoverage-methods0.2870.0200.308
getConfusionMatrix-methods0.0040.0080.012
getGenomicAnnot-methods0.0060.0080.014
getPeaks-methods0.0360.0080.044
getPredictorSignificance-methods0.0030.0080.011
getProbTreshold-methods0.0040.0070.011
getQuadProb-methods0.2520.0200.273
getTestedGapDistances-methods0.2150.0110.225
getTranscripts-methods0.2180.0100.228
peaksToBed-methods5.8030.2646.067
plotErrorRate-methods0.7160.0320.777
plotFeatures-methods1.8990.0135.985
plotGenomicAnnot-methods0.2660.0040.269
plotROC-methods1.3490.0241.375
predictStrand-methods6.3470.3586.707
predictTssOverlap-methods1.2200.0371.257
show0.2190.0200.238
transcriptsToBed-methods1.1730.0701.244