Package: GeneBreak

Version: 1.8.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings GeneBreak_1.8.0.tar.gz

StartedAt: 2018-04-12 04:06:20 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 04:09:33 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 193.0 seconds

RetCode: 0

Status:  OK

CheckDir: GeneBreak.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 GeneBreak_1.8.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/GeneBreak.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-apple-darwin15.6.0 (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 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
CopyNumberBreakPointGenes-class                 8.082  0.767   9.074
recurrentGenes-CopyNumberBreakPointGenes-method 6.760  0.687   7.597
bpPlot-CopyNumberBreakPoints-method             6.447  0.732   7.307
bpStats-CopyNumberBreakPoints-method            5.665  0.721   6.459
* 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
  ‘/Users/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	8.082	0.767	9.074
CopyNumberBreakPoints-class	1.636	0.200	1.875
accessOptions-CopyNumberBreakPoints-method	0.816	0.114	0.960
addGeneAnnotation-CopyNumberBreakPoints-method	2.903	0.201	3.178
bpFilter-CopyNumberBreakPoints-method	1.464	0.193	1.681
bpGenes-CopyNumberBreakPointGenes-method	2.741	0.223	3.046
bpPlot-CopyNumberBreakPoints-method	6.447	0.732	7.307
bpStats-CopyNumberBreakPoints-method	5.665	0.721	6.459
breakpointData-CopyNumberBreakPoints-method	1.233	0.417	1.681
breakpointsPerGene-CopyNumberBreakPointGenes-method	2.694	0.460	3.193
callData-CopyNumberBreakPoints-method	1.172	0.387	1.585
featureChromosomes-CopyNumberBreakPoints-method	0.824	0.144	0.982
featureInfo-CopyNumberBreakPoints-method	2.354	0.289	2.670
featuresPerGene-CopyNumberBreakPointGenes-method	2.414	0.204	2.635
geneChromosomes-CopyNumberBreakPointGenes-method	2.452	0.206	2.695
geneInfo-CopyNumberBreakPointGenes-method	2.691	0.249	3.002
getBreakpoints	1.723	0.185	1.948
namesFeatures-CopyNumberBreakPoints-method	0.828	0.116	0.966
recurrentGenes-CopyNumberBreakPointGenes-method	6.760	0.687	7.597
sampleNames-CopyNumberBreakPoints-method	0.871	0.150	1.056
segmentData-CopyNumberBreakPoints-method	1.598	0.478	2.134