BioC 3.5: CHECK report for JunctionSeq on oaxaca

Package: JunctionSeq

Version: 1.5.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings JunctionSeq_1.5.0.tar.gz

StartedAt: 2017-02-23 04:12:44 -0800 (Thu, 23 Feb 2017)

EndedAt: 2017-02-23 04:17:00 -0800 (Thu, 23 Feb 2017)

EllapsedTime: 255.8 seconds

RetCode: 0

Status:  OK

CheckDir: JunctionSeq.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings JunctionSeq_1.5.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/JunctionSeq.Rcheck’
* using R Under development (unstable) (2017-02-15 r72177)
* 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 ‘1.5.0’
* 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 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 ... 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 19.787  1.019  21.109
* 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
  ‘/Users/biocbuild/bbs-3.5-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	0.003	0.000	0.002
buildAllPlots	19.787	1.019	21.109
buildAllPlotsForGene	2.677	0.176	2.835
defaultColorList	2.258	0.171	2.414
estimateEffectSizes	4.716	0.042	4.769
estimateJunctionSeqDispersions	0.002	0.000	0.003
estimateJunctionSeqSizeFactors	0.223	0.006	0.229
fitJunctionSeqDispersionFunction	0.569	0.012	0.581
plotDispEsts	0.156	0.005	0.161
plotJunctionSeqResultsForGene	0.128	0.004	0.134
plotMA	1.001	0.041	1.044
readAnnotationData	0.911	0.006	0.958
readJunctionSeqCounts	1.093	0.021	1.175
runJunctionSeqAnalyses	0.002	0.000	0.002
testForDiffUsage	1.647	0.023	1.669
writeBedTrack	0.137	0.010	0.147
writeCompleteResults	0.623	0.009	0.632