Evert van den Broek
| Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018) |
| URL: https://git.bioconductor.org/packages/GeneBreak |
| Branch: RELEASE_3_7 |
| Last Commit: 1a55884 |
| Last Changed Date: 2018-04-30 10:35:38 -0400 (Mon, 30 Apr 2018) |
| Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 08:55:31 -0400 (Wed, 17 Oct 2018).
| Package 561/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| GeneBreak 1.10.0 Evert van den Broek
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: GeneBreak |
| Version: 1.10.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:GeneBreak.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings GeneBreak_1.10.0.tar.gz |
| StartedAt: 2018-10-16 21:33:38 -0400 (Tue, 16 Oct 2018) |
| EndedAt: 2018-10-16 21:36:44 -0400 (Tue, 16 Oct 2018) |
| EllapsedTime: 186.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: GeneBreak.Rcheck |
| Warnings: 0 |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:GeneBreak.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings GeneBreak_1.10.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/GeneBreak.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-apple-darwin15.6.0 (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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
CopyNumberBreakPointGenes-class 7.733 0.733 8.501
bpStats-CopyNumberBreakPoints-method 6.101 0.697 6.820
bpPlot-CopyNumberBreakPoints-method 6.049 0.582 6.664
recurrentGenes-CopyNumberBreakPointGenes-method 5.929 0.695 6.652
* 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
‘/Users/biocbuild/bbs-3.7-bioc/meat/GeneBreak.Rcheck/00check.log’
for details.
GeneBreak.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL GeneBreak ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/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)
GeneBreak.Rcheck/GeneBreak-Ex.timings
| name | user | system | elapsed | |
| CopyNumberBreakPointGenes-class | 7.733 | 0.733 | 8.501 | |
| CopyNumberBreakPoints-class | 1.624 | 0.179 | 1.806 | |
| accessOptions-CopyNumberBreakPoints-method | 0.930 | 0.140 | 1.074 | |
| addGeneAnnotation-CopyNumberBreakPoints-method | 1.953 | 0.251 | 2.212 | |
| bpFilter-CopyNumberBreakPoints-method | 1.397 | 0.230 | 1.636 | |
| bpGenes-CopyNumberBreakPointGenes-method | 2.371 | 0.247 | 2.627 | |
| bpPlot-CopyNumberBreakPoints-method | 6.049 | 0.582 | 6.664 | |
| bpStats-CopyNumberBreakPoints-method | 6.101 | 0.697 | 6.820 | |
| breakpointData-CopyNumberBreakPoints-method | 1.581 | 0.531 | 2.122 | |
| breakpointsPerGene-CopyNumberBreakPointGenes-method | 2.568 | 0.641 | 3.216 | |
| callData-CopyNumberBreakPoints-method | 1.603 | 0.491 | 2.103 | |
| featureChromosomes-CopyNumberBreakPoints-method | 0.972 | 0.157 | 1.137 | |
| featureInfo-CopyNumberBreakPoints-method | 2.418 | 0.308 | 2.734 | |
| featuresPerGene-CopyNumberBreakPointGenes-method | 2.473 | 0.239 | 2.725 | |
| geneChromosomes-CopyNumberBreakPointGenes-method | 2.079 | 0.254 | 2.343 | |
| geneInfo-CopyNumberBreakPointGenes-method | 2.072 | 0.263 | 2.342 | |
| getBreakpoints | 1.673 | 0.198 | 1.877 | |
| namesFeatures-CopyNumberBreakPoints-method | 0.954 | 0.117 | 1.081 | |
| recurrentGenes-CopyNumberBreakPointGenes-method | 5.929 | 0.695 | 6.652 | |
| sampleNames-CopyNumberBreakPoints-method | 0.686 | 0.138 | 0.827 | |
| segmentData-CopyNumberBreakPoints-method | 1.790 | 0.447 | 2.245 | |