Evert van den Broek
| Snapshot Date: 2020-01-15 16:46:30 -0500 (Wed, 15 Jan 2020) |
| URL: https://git.bioconductor.org/packages/GeneBreak |
| Branch: master |
| Last Commit: 39d1c8f |
| Last Changed Date: 2019-10-29 13:40:05 -0500 (Tue, 29 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-01-16 13:43:38 -0500 (Thu, 16 Jan 2020).
| Package 648/1818 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| GeneBreak 1.17.0 Evert van den Broek
| malbec2 | Linux (Ubuntu 18.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: GeneBreak |
| Version: 1.17.0 |
| 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_1.17.0.tar.gz |
| StartedAt: 2020-01-16 04:43:22 -0500 (Thu, 16 Jan 2020) |
| EndedAt: 2020-01-16 04:48:14 -0500 (Thu, 16 Jan 2020) |
| EllapsedTime: 292.6 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_1.17.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/GeneBreak.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* 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 ‘1.17.0’
* 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 (user + system) or elapsed time > 5s
user system elapsed
CopyNumberBreakPointGenes-class 10.298 2.046 12.349
recurrentGenes-CopyNumberBreakPointGenes-method 8.062 1.843 9.905
bpStats-CopyNumberBreakPoints-method 7.954 1.728 9.685
bpPlot-CopyNumberBreakPoints-method 7.831 1.775 9.607
* 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-3.11-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/4.0/Resources/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)
GeneBreak.Rcheck/GeneBreak-Ex.timings
| name | user | system | elapsed | |
| CopyNumberBreakPointGenes-class | 10.298 | 2.046 | 12.349 | |
| CopyNumberBreakPoints-class | 1.937 | 0.429 | 2.367 | |
| accessOptions-CopyNumberBreakPoints-method | 1.347 | 0.256 | 1.604 | |
| addGeneAnnotation-CopyNumberBreakPoints-method | 2.534 | 0.443 | 2.977 | |
| bpFilter-CopyNumberBreakPoints-method | 1.780 | 0.353 | 2.132 | |
| bpGenes-CopyNumberBreakPointGenes-method | 2.862 | 0.490 | 3.352 | |
| bpPlot-CopyNumberBreakPoints-method | 7.831 | 1.775 | 9.607 | |
| bpStats-CopyNumberBreakPoints-method | 7.954 | 1.728 | 9.685 | |
| breakpointData-CopyNumberBreakPoints-method | 1.670 | 1.101 | 2.771 | |
| breakpointsPerGene-CopyNumberBreakPointGenes-method | 3.613 | 1.239 | 4.853 | |
| callData-CopyNumberBreakPoints-method | 2.288 | 1.162 | 3.452 | |
| featureChromosomes-CopyNumberBreakPoints-method | 1.403 | 0.286 | 1.688 | |
| featureInfo-CopyNumberBreakPoints-method | 3.103 | 0.671 | 3.775 | |
| featuresPerGene-CopyNumberBreakPointGenes-method | 2.698 | 0.492 | 3.191 | |
| geneChromosomes-CopyNumberBreakPointGenes-method | 2.740 | 0.417 | 3.157 | |
| geneInfo-CopyNumberBreakPointGenes-method | 2.703 | 0.602 | 3.305 | |
| getBreakpoints | 2.435 | 0.442 | 2.878 | |
| namesFeatures-CopyNumberBreakPoints-method | 0.909 | 0.257 | 1.165 | |
| recurrentGenes-CopyNumberBreakPointGenes-method | 8.062 | 1.843 | 9.905 | |
| sampleNames-CopyNumberBreakPoints-method | 0.843 | 0.262 | 1.106 | |
| segmentData-CopyNumberBreakPoints-method | 1.730 | 1.011 | 2.760 | |