Package: GeneBreak

Version: 1.8.0

Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings GeneBreak_1.8.0.tar.gz

StartedAt: 2018-04-11 23:42:25 -0400 (Wed, 11 Apr 2018)

EndedAt: 2018-04-11 23:45:08 -0400 (Wed, 11 Apr 2018)

EllapsedTime: 163.1 seconds

RetCode: 0

Status:  OK

CheckDir: GeneBreak.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings GeneBreak_1.8.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/GeneBreak.Rcheck’
* using R version 3.4.4 (2018-03-15)
* 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 ‘1.8.0’
* 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      7.000  0.092   7.096
bpPlot-CopyNumberBreakPoints-method  5.456  0.016   5.480
bpStats-CopyNumberBreakPoints-method 5.304  0.024   5.334
* 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-3.6-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	7.000	0.092	7.096
CopyNumberBreakPoints-class	1.692	0.080	1.778
accessOptions-CopyNumberBreakPoints-method	1.064	0.032	1.098
addGeneAnnotation-CopyNumberBreakPoints-method	2.636	0.048	2.686
bpFilter-CopyNumberBreakPoints-method	1.488	0.040	1.529
bpGenes-CopyNumberBreakPointGenes-method	2.932	0.016	2.951
bpPlot-CopyNumberBreakPoints-method	5.456	0.016	5.480
bpStats-CopyNumberBreakPoints-method	5.304	0.024	5.334
breakpointData-CopyNumberBreakPoints-method	1.184	0.180	1.364
breakpointsPerGene-CopyNumberBreakPointGenes-method	3.196	0.196	3.401
callData-CopyNumberBreakPoints-method	1.052	0.204	1.259
featureChromosomes-CopyNumberBreakPoints-method	0.776	0.036	0.812
featureInfo-CopyNumberBreakPoints-method	2.564	0.056	2.621
featuresPerGene-CopyNumberBreakPointGenes-method	2.536	0.040	2.579
geneChromosomes-CopyNumberBreakPointGenes-method	2.340	0.028	2.369
geneInfo-CopyNumberBreakPointGenes-method	2.500	0.044	2.545
getBreakpoints	1.264	0.028	1.294
namesFeatures-CopyNumberBreakPoints-method	0.728	0.036	0.768
recurrentGenes-CopyNumberBreakPointGenes-method	4.704	0.024	4.731
sampleNames-CopyNumberBreakPoints-method	0.700	0.016	0.718
segmentData-CopyNumberBreakPoints-method	1.356	0.192	1.550