BioC 3.4: CHECK report for GeneBreak on malbec1

Package: GeneBreak

Version: 1.4.0

Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings GeneBreak_1.4.0.tar.gz

StartedAt: 2017-04-14 22:42:00 -0400 (Fri, 14 Apr 2017)

EndedAt: 2017-04-14 22:44:38 -0400 (Fri, 14 Apr 2017)

EllapsedTime: 159.0 seconds

RetCode: 0

Status:  OK

CheckDir: GeneBreak.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 GeneBreak_1.4.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/GeneBreak.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GeneBreak/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GeneBreak’ version ‘1.4.0’
* 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 ‘GeneBreak’ 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
.glmbreak: no visible global function definition for ‘glm’
.glmbreak: no visible global function definition for ‘predict’
addGeneAnnotation,CopyNumberBreakPoints: no visible global function
  definition for ‘head’
bpStats,CopyNumberBreakPoints: no visible global function definition
  for ‘sd’
bpStats,CopyNumberBreakPoints: no visible global function definition
  for ‘p.adjust’
Undefined global functions or variables:
  glm head p.adjust predict sd
Consider adding
  importFrom("stats", "glm", "p.adjust", "predict", "sd")
  importFrom("utils", "head")
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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... 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
CopyNumberBreakPointGenes-class                 7.628  0.064   7.701
bpStats-CopyNumberBreakPoints-method            6.420  0.000   6.425
bpPlot-CopyNumberBreakPoints-method             5.920  0.020   5.944
recurrentGenes-CopyNumberBreakPointGenes-method 5.888  0.016   5.908
* 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
  ‘/home/biocbuild/bbs-3.4-bioc/meat/GeneBreak.Rcheck/00check.log’
for details.

* installing *source* package ‘GeneBreak’ ...
** R
** data
** inst
** preparing package for lazy loading
Creating a new generic function for ‘segmentData’ in package ‘GeneBreak’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (GeneBreak)

name	user	system	elapsed
CopyNumberBreakPointGenes-class	7.628	0.064	7.701
CopyNumberBreakPoints-class	1.712	0.024	1.736
accessOptions-CopyNumberBreakPoints-method	0.948	0.004	0.952
addGeneAnnotation-CopyNumberBreakPoints-method	2.424	0.008	2.434
bpFilter-CopyNumberBreakPoints-method	1.148	0.012	1.161
bpGenes-CopyNumberBreakPointGenes-method	2.712	0.024	2.736
bpPlot-CopyNumberBreakPoints-method	5.920	0.020	5.944
bpStats-CopyNumberBreakPoints-method	6.420	0.000	6.425
breakpointData-CopyNumberBreakPoints-method	0.980	0.152	1.131
breakpointsPerGene-CopyNumberBreakPointGenes-method	2.664	0.120	2.785
callData-CopyNumberBreakPoints-method	1.096	0.128	1.225
featureChromosomes-CopyNumberBreakPoints-method	0.836	0.016	0.853
featureInfo-CopyNumberBreakPoints-method	2.584	0.040	2.628
featuresPerGene-CopyNumberBreakPointGenes-method	2.464	0.016	2.480
geneChromosomes-CopyNumberBreakPointGenes-method	2.688	0.012	2.702
geneInfo-CopyNumberBreakPointGenes-method	2.32	0.02	2.34
getBreakpoints	1.580	0.020	1.599
namesFeatures-CopyNumberBreakPoints-method	0.824	0.008	0.834
recurrentGenes-CopyNumberBreakPointGenes-method	5.888	0.016	5.908
sampleNames-CopyNumberBreakPoints-method	0.888	0.000	0.889
segmentData-CopyNumberBreakPoints-method	1.104	0.128	1.231