Evert van den Broek
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/GeneBreak |
| Branch: RELEASE_3_9 |
| Last Commit: 116ace4 |
| Last Changed Date: 2019-05-02 11:53:58 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:56:37 -0400 (Wed, 16 Oct 2019).
| Package 624/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| GeneBreak 1.14.0 Evert van den Broek
| malbec2 | Linux (Ubuntu 18.04.2 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: 1.14.0 |
| 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_1.14.0.tar.gz |
| StartedAt: 2019-10-16 03:02:27 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 03:06:54 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 266.2 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_1.14.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/GeneBreak.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.14.0’
* 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 10.507 1.982 12.495
bpPlot-CopyNumberBreakPoints-method 8.433 1.818 10.259
bpStats-CopyNumberBreakPoints-method 7.894 1.713 9.619
recurrentGenes-CopyNumberBreakPointGenes-method 7.567 1.619 9.187
breakpointsPerGene-CopyNumberBreakPointGenes-method 3.694 1.324 5.019
* 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-3.9-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/3.6/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 | 10.507 | 1.982 | 12.495 | |
| CopyNumberBreakPoints-class | 2.309 | 0.343 | 2.652 | |
| accessOptions-CopyNumberBreakPoints-method | 1.379 | 0.217 | 1.596 | |
| addGeneAnnotation-CopyNumberBreakPoints-method | 2.877 | 0.394 | 3.273 | |
| bpFilter-CopyNumberBreakPoints-method | 1.776 | 0.343 | 2.119 | |
| bpGenes-CopyNumberBreakPointGenes-method | 3.001 | 0.436 | 3.437 | |
| bpPlot-CopyNumberBreakPoints-method | 8.433 | 1.818 | 10.259 | |
| bpStats-CopyNumberBreakPoints-method | 7.894 | 1.713 | 9.619 | |
| breakpointData-CopyNumberBreakPoints-method | 2.236 | 1.097 | 3.336 | |
| breakpointsPerGene-CopyNumberBreakPointGenes-method | 3.694 | 1.324 | 5.019 | |
| callData-CopyNumberBreakPoints-method | 2.285 | 0.964 | 3.251 | |
| featureChromosomes-CopyNumberBreakPoints-method | 1.460 | 0.256 | 1.715 | |
| featureInfo-CopyNumberBreakPoints-method | 3.429 | 0.690 | 4.123 | |
| featuresPerGene-CopyNumberBreakPointGenes-method | 3.093 | 0.410 | 3.508 | |
| geneChromosomes-CopyNumberBreakPointGenes-method | 2.752 | 0.498 | 3.252 | |
| geneInfo-CopyNumberBreakPointGenes-method | 2.600 | 0.471 | 3.072 | |
| getBreakpoints | 2.082 | 0.375 | 2.457 | |
| namesFeatures-CopyNumberBreakPoints-method | 1.154 | 0.275 | 1.428 | |
| recurrentGenes-CopyNumberBreakPointGenes-method | 7.567 | 1.619 | 9.187 | |
| sampleNames-CopyNumberBreakPoints-method | 1.698 | 0.266 | 1.965 | |
| segmentData-CopyNumberBreakPoints-method | 2.077 | 0.954 | 3.031 | |