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BioC 3.5: CHECK report for JunctionSeq on malbec2

This page was generated on 2017-08-16 13:17:14 -0400 (Wed, 16 Aug 2017).

Package 697/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
JunctionSeq 1.6.0
Stephen Hartley
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/JunctionSeq
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: JunctionSeq
Version: 1.6.0
Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings JunctionSeq_1.6.0.tar.gz
StartedAt: 2017-08-16 00:06:34 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 00:09:48 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 193.3 seconds
RetCode: 0
Status:  OK 
CheckDir: JunctionSeq.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings JunctionSeq_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/JunctionSeq.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 ‘JunctionSeq/DESCRIPTION’ ... OK
* this is package ‘JunctionSeq’ version ‘1.6.0’
* 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 ‘JunctionSeq’ 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 ... NOTE
Foreign function calls to a different package:
  .Call("DESeq2_fitBeta", ..., PACKAGE = "DESeq2")
  .Call("DESeq2_fitDisp", ..., PACKAGE = "DESeq2")
  .Call("DESeq2_fitDispGrid", ..., PACKAGE = "DESeq2")
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
* checking R code for possible problems ... NOTE
testFeatureForDJU.fromRow.simpleNormDist: no visible global function
  definition for ‘glm.fit’
Undefined global functions or variables:
  glm.fit
Consider adding
  importFrom("stats", "glm.fit")
to your NAMESPACE file.
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                user system elapsed
buildAllPlots 14.176  0.192  14.471
* 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.5-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-class0.0000.0040.003
buildAllPlots14.176 0.19214.471
buildAllPlotsForGene1.5200.0001.522
defaultColorList1.4440.0121.458
estimateEffectSizes3.2600.0003.265
estimateJunctionSeqDispersions0.0040.0000.001
estimateJunctionSeqSizeFactors0.2200.0040.225
fitJunctionSeqDispersionFunction0.5960.0000.596
plotDispEsts0.7040.0000.708
plotJunctionSeqResultsForGene0.0880.0040.094
plotMA0.7640.0000.765
readAnnotationData0.5280.0000.554
readJunctionSeqCounts0.7960.0000.818
runJunctionSeqAnalyses0.0000.0000.001
testForDiffUsage1.0880.0001.089
writeBedTrack0.0680.0000.069
writeCompleteResults0.8840.0040.890