Back to Multiple platform build/check report for BioC 3.13
ABCDEF[G]HIJKLMNOPQRSTUVWXYZ

This page was generated on 2021-10-15 15:05:41 -0400 (Fri, 15 Oct 2021).

CHECK results for GeneBreak on nebbiolo1

To the developers/maintainers of the GeneBreak package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GeneBreak.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 710/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GeneBreak 1.22.0  (landing page)
Evert van den Broek
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/GeneBreak
git_branch: RELEASE_3_13
git_last_commit: 4c84ab8
git_last_commit_date: 2021-05-19 12:16:21 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: GeneBreak
Version: 1.22.0
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:GeneBreak.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings GeneBreak_1.22.0.tar.gz
StartedAt: 2021-10-14 09:56:03 -0400 (Thu, 14 Oct 2021)
EndedAt: 2021-10-14 09:58:35 -0400 (Thu, 14 Oct 2021)
EllapsedTime: 151.3 seconds
RetCode: 0
Status:   OK  
CheckDir: GeneBreak.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:GeneBreak.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings GeneBreak_1.22.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/GeneBreak.Rcheck’
* using R version 4.1.1 (2021-08-10)
* 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 ‘1.22.0’
* 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 (user + system) or elapsed time > 5s
                                     user system elapsed
CopyNumberBreakPointGenes-class     5.525  0.168   5.694
bpPlot-CopyNumberBreakPoints-method 4.929  0.344   5.274
* 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-3.13-bioc/meat/GeneBreak.Rcheck/00check.log’
for details.



Installation output

GeneBreak.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL GeneBreak
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.13-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)

Tests output


Example timings

GeneBreak.Rcheck/GeneBreak-Ex.timings

nameusersystemelapsed
CopyNumberBreakPointGenes-class5.5250.1685.694
CopyNumberBreakPoints-class1.7110.0961.807
accessOptions-CopyNumberBreakPoints-method0.9160.0440.961
addGeneAnnotation-CopyNumberBreakPoints-method1.8140.0721.887
bpFilter-CopyNumberBreakPoints-method1.4990.0481.549
bpGenes-CopyNumberBreakPointGenes-method2.8970.2763.174
bpPlot-CopyNumberBreakPoints-method4.9290.3445.274
bpStats-CopyNumberBreakPoints-method4.1500.0724.223
breakpointData-CopyNumberBreakPoints-method0.7110.7641.475
breakpointsPerGene-CopyNumberBreakPointGenes-method1.8380.7242.562
callData-CopyNumberBreakPoints-method1.1540.7721.925
featureChromosomes-CopyNumberBreakPoints-method0.9840.0441.028
featureInfo-CopyNumberBreakPoints-method1.7290.2161.945
featuresPerGene-CopyNumberBreakPointGenes-method1.6830.0081.692
geneChromosomes-CopyNumberBreakPointGenes-method1.2320.0431.274
geneInfo-CopyNumberBreakPointGenes-method1.5850.0921.678
getBreakpoints1.2990.0601.360
namesFeatures-CopyNumberBreakPoints-method0.9780.0721.049
recurrentGenes-CopyNumberBreakPointGenes-method4.2410.0354.277
sampleNames-CopyNumberBreakPoints-method0.9000.0440.945
segmentData-CopyNumberBreakPoints-method1.1430.7561.898