Package: GeneBreak

Version: 1.12.0

Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:GeneBreak.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings GeneBreak_1.12.0.tar.gz

StartedAt: 2019-04-16 00:06:35 -0400 (Tue, 16 Apr 2019)

EndedAt: 2019-04-16 00:09:22 -0400 (Tue, 16 Apr 2019)

EllapsedTime: 167.4 seconds

RetCode: 0

Status:  OK

CheckDir: GeneBreak.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:GeneBreak.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings GeneBreak_1.12.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/GeneBreak.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘1.12.0’
* 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 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                                     user system elapsed
CopyNumberBreakPointGenes-class     7.320  0.092   7.435
bpPlot-CopyNumberBreakPoints-method 6.144  0.044   6.216
* 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-3.8-bioc/meat/GeneBreak.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL GeneBreak
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* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’
* installing *source* package ‘GeneBreak’ ...
** R
** data
** byte-compile and prepare 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	7.320	0.092	7.435
CopyNumberBreakPoints-class	1.408	0.064	1.471
accessOptions-CopyNumberBreakPoints-method	1.184	0.024	1.209
addGeneAnnotation-CopyNumberBreakPoints-method	2.728	0.028	2.762
bpFilter-CopyNumberBreakPoints-method	1.672	0.048	1.722
bpGenes-CopyNumberBreakPointGenes-method	1.936	0.016	1.956
bpPlot-CopyNumberBreakPoints-method	6.144	0.044	6.216
bpStats-CopyNumberBreakPoints-method	4.464	0.032	4.498
breakpointData-CopyNumberBreakPoints-method	1.328	0.256	1.584
breakpointsPerGene-CopyNumberBreakPointGenes-method	2.376	0.176	2.555
callData-CopyNumberBreakPoints-method	1.008	0.208	1.222
featureChromosomes-CopyNumberBreakPoints-method	1.016	0.032	1.050
featureInfo-CopyNumberBreakPoints-method	2.328	0.100	2.429
featuresPerGene-CopyNumberBreakPointGenes-method	2.028	0.044	2.076
geneChromosomes-CopyNumberBreakPointGenes-method	2.368	0.036	2.427
geneInfo-CopyNumberBreakPointGenes-method	2.224	0.040	2.268
getBreakpoints	2.020	0.024	2.050
namesFeatures-CopyNumberBreakPoints-method	1.128	0.032	1.164
recurrentGenes-CopyNumberBreakPointGenes-method	4.688	0.048	4.743
sampleNames-CopyNumberBreakPoints-method	0.956	0.036	0.993
segmentData-CopyNumberBreakPoints-method	0.932	0.200	1.133