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BioC 3.3: CHECK report for JunctionSeq on morelia

This page was generated on 2016-04-21 13:27:42 -0700 (Thu, 21 Apr 2016).

Package 612/1210HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
JunctionSeq 1.1.17
Stephen Hartley
Snapshot Date: 2016-04-20 17:20:35 -0700 (Wed, 20 Apr 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/JunctionSeq
Last Changed Rev: 114654 / Revision: 116626
Last Changed Date: 2016-03-11 12:22:28 -0800 (Fri, 11 Mar 2016)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (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: JunctionSeq
Version: 1.1.17
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings JunctionSeq_1.1.17.tar.gz
StartedAt: 2016-04-21 04:18:31 -0700 (Thu, 21 Apr 2016)
EndedAt: 2016-04-21 04:22:15 -0700 (Thu, 21 Apr 2016)
EllapsedTime: 224.5 seconds
RetCode: 0
Status:  OK 
CheckDir: JunctionSeq.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings JunctionSeq_1.1.17.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/JunctionSeq.Rcheck’
* using R version 3.3.0 beta (2016-04-06 r70435)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘JunctionSeq/DESCRIPTION’ ... OK
* this is package ‘JunctionSeq’ version ‘1.1.17’
* 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 ‘JunctionSeq’ can be installed ... [17s/17s] 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 ... NOTE
Foreign function calls to a different package:
  .Call("DESeq2_fitBeta", ..., PACKAGE = "DESeq2")
  .Call("DESeq2_fitDisp", ..., PACKAGE = "DESeq2")
  .Call("DESeq2_fitDispGrid", ..., PACKAGE = "DESeq2")
  .Call("DESeq2_rlogGrid", ..., PACKAGE = "DESeq2")
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [38s/39s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
buildAllPlots 17.32  0.964  18.663
* 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-3.3-bioc/meat/JunctionSeq.Rcheck/00check.log’
for details.


JunctionSeq.Rcheck/00install.out:

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

JunctionSeq.Rcheck/JunctionSeq-Ex.timings:

nameusersystemelapsed
JunctionSeqCountSet-class0.0040.0010.004
buildAllPlots17.320 0.96418.663
buildAllPlotsForGene2.0170.1362.139
defaultColorList2.2350.1592.375
estimateEffectSizes3.5430.0103.792
estimateJunctionSeqDispersions0.0010.0000.001
estimateJunctionSeqSizeFactors0.3240.0050.329
fitJunctionSeqDispersionFunction0.4080.0070.416
plotDispEsts0.0650.0030.068
plotJunctionSeqResultsForGene0.1240.0060.130
plotMA0.3770.0240.402
readAnnotationData0.7170.0100.782
readJunctionSeqCounts0.5710.0040.851
runJunctionSeqAnalyses0.0010.0000.002
testForDiffUsage0.5630.0100.573
writeBedTrack0.0730.0020.075
writeCompleteResults0.6050.0090.614