Evert van den Broek
| Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019) |
| URL: https://git.bioconductor.org/packages/GeneBreak |
| Branch: RELEASE_3_8 |
| Last Commit: 7437a2c |
| Last Changed Date: 2018-10-30 11:41:59 -0400 (Tue, 30 Oct 2018) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-16 11:59:03 -0400 (Tue, 16 Apr 2019).
| Package 592/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| GeneBreak 1.12.0 Evert van den Broek
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: GeneBreak |
| Version: 1.12.0 |
| 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_1.12.0.tar.gz |
| StartedAt: 2019-04-16 00:07:06 -0400 (Tue, 16 Apr 2019) |
| EndedAt: 2019-04-16 00:10:43 -0400 (Tue, 16 Apr 2019) |
| EllapsedTime: 216.9 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_1.12.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/GeneBreak.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘1.12.0’
* 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 6.478 0.811 7.310
bpPlot-CopyNumberBreakPoints-method 6.716 0.539 7.293
recurrentGenes-CopyNumberBreakPointGenes-method 6.409 0.740 7.188
bpStats-CopyNumberBreakPoints-method 6.190 0.680 6.918
* 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-3.8-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 | 6.478 | 0.811 | 7.310 | |
| CopyNumberBreakPoints-class | 1.720 | 0.166 | 1.890 | |
| accessOptions-CopyNumberBreakPoints-method | 1.022 | 0.157 | 1.182 | |
| addGeneAnnotation-CopyNumberBreakPoints-method | 2.254 | 0.272 | 2.537 | |
| bpFilter-CopyNumberBreakPoints-method | 1.526 | 0.244 | 1.776 | |
| bpGenes-CopyNumberBreakPointGenes-method | 2.811 | 0.262 | 3.084 | |
| bpPlot-CopyNumberBreakPoints-method | 6.716 | 0.539 | 7.293 | |
| bpStats-CopyNumberBreakPoints-method | 6.190 | 0.680 | 6.918 | |
| breakpointData-CopyNumberBreakPoints-method | 1.590 | 0.569 | 2.166 | |
| breakpointsPerGene-CopyNumberBreakPointGenes-method | 2.724 | 0.635 | 3.374 | |
| callData-CopyNumberBreakPoints-method | 1.709 | 0.531 | 2.251 | |
| featureChromosomes-CopyNumberBreakPoints-method | 0.974 | 0.163 | 1.146 | |
| featureInfo-CopyNumberBreakPoints-method | 2.624 | 0.308 | 2.946 | |
| featuresPerGene-CopyNumberBreakPointGenes-method | 2.628 | 0.251 | 2.890 | |
| geneChromosomes-CopyNumberBreakPointGenes-method | 2.408 | 0.216 | 2.636 | |
| geneInfo-CopyNumberBreakPointGenes-method | 2.351 | 0.297 | 2.668 | |
| getBreakpoints | 1.851 | 0.231 | 2.098 | |
| namesFeatures-CopyNumberBreakPoints-method | 0.796 | 0.162 | 0.961 | |
| recurrentGenes-CopyNumberBreakPointGenes-method | 6.409 | 0.740 | 7.188 | |
| sampleNames-CopyNumberBreakPoints-method | 1.111 | 0.180 | 1.296 | |
| segmentData-CopyNumberBreakPoints-method | 1.425 | 0.567 | 2.009 | |