Package: GeneBreak

Version: 1.10.0

Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:GeneBreak.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings GeneBreak_1.10.0.tar.gz

StartedAt: 2018-10-16 00:37:36 -0400 (Tue, 16 Oct 2018)

EndedAt: 2018-10-16 00:39:44 -0400 (Tue, 16 Oct 2018)

EllapsedTime: 128.1 seconds

RetCode: 0

Status:  OK

CheckDir: GeneBreak.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:GeneBreak.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings GeneBreak_1.10.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/GeneBreak.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* 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 ‘1.10.0’
* 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 5.036   0.08   5.122
* 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-3.7-bioc/meat/GeneBreak.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL GeneBreak
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* installing to library ‘/home/biocbuild/bbs-3.7-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	5.036	0.080	5.122
CopyNumberBreakPoints-class	1.168	0.048	1.216
accessOptions-CopyNumberBreakPoints-method	0.732	0.040	0.771
addGeneAnnotation-CopyNumberBreakPoints-method	1.852	0.008	1.862
bpFilter-CopyNumberBreakPoints-method	1.376	0.040	1.415
bpGenes-CopyNumberBreakPointGenes-method	1.968	0.008	1.980
bpPlot-CopyNumberBreakPoints-method	4.520	0.040	4.565
bpStats-CopyNumberBreakPoints-method	4.024	0.032	4.058
breakpointData-CopyNumberBreakPoints-method	0.980	0.156	1.139
breakpointsPerGene-CopyNumberBreakPointGenes-method	1.772	0.140	1.917
callData-CopyNumberBreakPoints-method	0.980	0.196	1.181
featureChromosomes-CopyNumberBreakPoints-method	0.772	0.020	0.791
featureInfo-CopyNumberBreakPoints-method	2.072	0.060	2.133
featuresPerGene-CopyNumberBreakPointGenes-method	1.612	0.028	1.642
geneChromosomes-CopyNumberBreakPointGenes-method	1.616	0.008	1.627
geneInfo-CopyNumberBreakPointGenes-method	1.556	0.040	1.598
getBreakpoints	1.396	0.048	1.446
namesFeatures-CopyNumberBreakPoints-method	0.796	0.028	0.826
recurrentGenes-CopyNumberBreakPointGenes-method	4.132	0.032	4.168
sampleNames-CopyNumberBreakPoints-method	0.836	0.016	0.854
segmentData-CopyNumberBreakPoints-method	1.132	0.148	1.284