BioC 3.5: CHECK report for segmentSeq on oaxaca

Package: segmentSeq

Version: 2.9.5

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings segmentSeq_2.9.5.tar.gz

StartedAt: 2017-01-29 07:03:42 -0800 (Sun, 29 Jan 2017)

EndedAt: 2017-01-29 07:43:43 -0800 (Sun, 29 Jan 2017)

EllapsedTime: 2400.4 seconds

RetCode: None

Status:  TIMEOUT

CheckDir: segmentSeq.Rcheck

Warnings: NA

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings segmentSeq_2.9.5.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/segmentSeq.Rcheck’
* using R Under development (unstable) (2016-10-26 r71594)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘segmentSeq/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘segmentSeq’ version ‘2.9.5’
* 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 ‘segmentSeq’ 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 ... NOTE
.lociLikelihoods: no visible binding for global variable ‘countLoci’
.massiveClassifyNulls: no visible global function definition for
  ‘getPriors.BB’
Undefined global functions or variables:
  countLoci getPriors.BB
* 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 ...

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

name	user	system	elapsed
alignmentData-class	2.131	0.023	2.154
classifySeg	27.371	0.110	27.498
findChunks	2.041	0.021	2.062
getCounts	3.216	0.014	3.232
getOverlaps	2.289	0.006	2.297
heuristicSeg	10.596	0.019	10.616
lociLikelihoods	13.709	0.039	13.783
normaliseNC	10.360	0.487	10.867
plotGenome	5.305	0.030	5.339
processAD	3.017	0.026	3.045
readMethods	2.268	0.015	2.284
readMeths	8.809	0.478	9.293
segData-class	3.153	0.028	3.184
segmentSeq-package	2.999	0.012	3.012