Package: GeneBreak

Version: 1.16.0

Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:GeneBreak.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings GeneBreak_1.16.0.tar.gz

StartedAt: 2020-04-15 03:24:35 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 03:27:31 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 175.7 seconds

RetCode: 0

Status:  OK

CheckDir: GeneBreak.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:GeneBreak.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings GeneBreak_1.16.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/GeneBreak.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘1.16.0’
* 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                 7.304  0.148   7.464
recurrentGenes-CopyNumberBreakPointGenes-method 6.920  0.044   6.968
bpPlot-CopyNumberBreakPoints-method             6.060  0.028   6.097
bpStats-CopyNumberBreakPoints-method            5.336  0.036   5.374
* 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-3.10-bioc/meat/GeneBreak.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL GeneBreak
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* installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/library’
* installing *source* package ‘GeneBreak’ ...
** using staged installation
** 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 from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (GeneBreak)

name	user	system	elapsed
CopyNumberBreakPointGenes-class	7.304	0.148	7.464
CopyNumberBreakPoints-class	1.516	0.088	1.615
accessOptions-CopyNumberBreakPoints-method	1.456	0.020	1.480
addGeneAnnotation-CopyNumberBreakPoints-method	2.392	0.012	2.405
bpFilter-CopyNumberBreakPoints-method	1.560	0.032	1.601
bpGenes-CopyNumberBreakPointGenes-method	1.836	0.020	1.860
bpPlot-CopyNumberBreakPoints-method	6.060	0.028	6.097
bpStats-CopyNumberBreakPoints-method	5.336	0.036	5.374
breakpointData-CopyNumberBreakPoints-method	1.016	0.144	1.162
breakpointsPerGene-CopyNumberBreakPointGenes-method	2.480	0.236	2.722
callData-CopyNumberBreakPoints-method	1.128	0.224	1.354
featureChromosomes-CopyNumberBreakPoints-method	1.128	0.036	1.161
featureInfo-CopyNumberBreakPoints-method	2.172	0.064	2.238
featuresPerGene-CopyNumberBreakPointGenes-method	2.196	0.032	2.232
geneChromosomes-CopyNumberBreakPointGenes-method	2.312	0.024	2.338
geneInfo-CopyNumberBreakPointGenes-method	2.360	0.040	2.405
getBreakpoints	1.540	0.032	1.576
namesFeatures-CopyNumberBreakPoints-method	1.076	0.036	1.119
recurrentGenes-CopyNumberBreakPointGenes-method	6.920	0.044	6.968
sampleNames-CopyNumberBreakPoints-method	0.960	0.016	0.977
segmentData-CopyNumberBreakPoints-method	1.004	0.208	1.212