Back to Multiple platform build/check report for BioC 3.16:   simplified   long
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This page was generated on 2023-02-07 11:06:10 -0500 (Tue, 07 Feb 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_644.2.2 (2022-10-31) -- "Innocent and Trusting" 4511
palomino4Windows Server 2022 Datacenterx644.2.2 (2022-10-31 ucrt) -- "Innocent and Trusting" 4289
lconwaymacOS 12.5.1 Montereyx86_644.2.2 (2022-10-31) -- "Innocent and Trusting" 4318
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for GeneBreak on palomino4


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? 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 753/2183HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GeneBreak 1.28.0  (landing page)
Evert van den Broek
Snapshot Date: 2023-02-06 14:00:04 -0500 (Mon, 06 Feb 2023)
git_url: https://git.bioconductor.org/packages/GeneBreak
git_branch: RELEASE_3_16
git_last_commit: 1cc8091
git_last_commit_date: 2022-11-01 11:12:24 -0500 (Tue, 01 Nov 2022)
nebbiolo2Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.5.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: GeneBreak
Version: 1.28.0
Command: F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:GeneBreak.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings GeneBreak_1.28.0.tar.gz
StartedAt: 2023-02-07 01:39:22 -0500 (Tue, 07 Feb 2023)
EndedAt: 2023-02-07 01:42:05 -0500 (Tue, 07 Feb 2023)
EllapsedTime: 162.8 seconds
RetCode: 0
Status:   OK  
CheckDir: GeneBreak.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:GeneBreak.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings GeneBreak_1.28.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.16-bioc/meat/GeneBreak.Rcheck'
* using R version 4.2.2 (2022-10-31 ucrt)
* using platform: x86_64-w64-mingw32 (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 '1.28.0'
* 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 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 sizes of PDF files under 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                     user system elapsed
CopyNumberBreakPointGenes-class      5.82   0.43    6.25
bpStats-CopyNumberBreakPoints-method 5.36   0.08    5.44
* 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
  'F:/biocbuild/bbs-3.16-bioc/meat/GeneBreak.Rcheck/00check.log'
for details.



Installation output

GeneBreak.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL GeneBreak
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.16-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-class5.820.436.25
CopyNumberBreakPoints-class1.620.071.70
accessOptions-CopyNumberBreakPoints-method1.190.081.26
addGeneAnnotation-CopyNumberBreakPoints-method1.720.141.86
bpFilter-CopyNumberBreakPoints-method1.020.051.06
bpGenes-CopyNumberBreakPointGenes-method1.390.161.55
bpPlot-CopyNumberBreakPoints-method4.250.204.45
bpStats-CopyNumberBreakPoints-method5.360.085.44
breakpointData-CopyNumberBreakPoints-method1.030.371.40
breakpointsPerGene-CopyNumberBreakPointGenes-method1.560.421.99
callData-CopyNumberBreakPoints-method1.130.381.50
featureChromosomes-CopyNumberBreakPoints-method0.760.050.81
featureInfo-CopyNumberBreakPoints-method1.880.152.04
featuresPerGene-CopyNumberBreakPointGenes-method1.400.161.56
geneChromosomes-CopyNumberBreakPointGenes-method1.770.111.87
geneInfo-CopyNumberBreakPointGenes-method1.120.111.24
getBreakpoints1.490.061.54
namesFeatures-CopyNumberBreakPoints-method0.780.080.86
recurrentGenes-CopyNumberBreakPointGenes-method4.090.144.24
sampleNames-CopyNumberBreakPoints-method0.460.030.48
segmentData-CopyNumberBreakPoints-method0.840.301.14