BioC 3.4: CHECK report for JunctionSeq on zin1

Package: JunctionSeq

Version: 1.3.4

Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings JunctionSeq_1.3.4.tar.gz

StartedAt: 2016-09-20 08:27:50 -0700 (Tue, 20 Sep 2016)

EndedAt: 2016-09-20 08:30:31 -0700 (Tue, 20 Sep 2016)

EllapsedTime: 161.0 seconds

RetCode: 0

Status:  OK

CheckDir: JunctionSeq.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings JunctionSeq_1.3.4.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/JunctionSeq.Rcheck’
* using R version 3.3.1 (2016-06-21)
* 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 ‘1.3.4’
* 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")
  .Call("DESeq2_rlogGrid", ..., 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 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
buildAllPlots 11.708  0.068  11.855
* 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-3.4-bioc/meat/JunctionSeq.Rcheck/00check.log’
for details.

* 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)

name	user	system	elapsed
JunctionSeqCountSet-class	0.000	0.004	0.003
buildAllPlots	11.708	0.068	11.855
buildAllPlotsForGene	1.620	0.000	1.616
defaultColorList	1.880	0.000	1.884
estimateEffectSizes	3.260	0.000	3.259
estimateJunctionSeqDispersions	0.000	0.000	0.002
estimateJunctionSeqSizeFactors	0.128	0.000	0.131
fitJunctionSeqDispersionFunction	0.724	0.000	0.726
plotDispEsts	0.068	0.000	0.066
plotJunctionSeqResultsForGene	0.112	0.000	0.109
plotMA	0.524	0.004	0.528
readAnnotationData	0.552	0.000	0.560
readJunctionSeqCounts	0.420	0.004	0.450
runJunctionSeqAnalyses	0.000	0.000	0.001
testForDiffUsage	0.728	0.000	0.731
writeBedTrack	0.064	0.000	0.067
writeCompleteResults	0.604	0.004	0.609