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BioC 3.4: CHECK report for GeneBreak on malbec1

This page was generated on 2017-04-15 16:13:19 -0400 (Sat, 15 Apr 2017).

Package 480/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GeneBreak 1.4.0
Evert van den Broek
Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/GeneBreak
Last Changed Rev: 122710 / Revision: 128728
Last Changed Date: 2016-10-17 14:45:06 -0400 (Mon, 17 Oct 2016)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: GeneBreak
Version: 1.4.0
Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings GeneBreak_1.4.0.tar.gz
StartedAt: 2017-04-14 22:42:00 -0400 (Fri, 14 Apr 2017)
EndedAt: 2017-04-14 22:44:38 -0400 (Fri, 14 Apr 2017)
EllapsedTime: 159.0 seconds
RetCode: 0
Status:  OK 
CheckDir: GeneBreak.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings GeneBreak_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/GeneBreak.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-pc-linux-gnu (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 ‘1.4.0’
* 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 loading without being on the library search path ... 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                                                 user system elapsed
CopyNumberBreakPointGenes-class                 7.628  0.064   7.701
bpStats-CopyNumberBreakPoints-method            6.420  0.000   6.425
bpPlot-CopyNumberBreakPoints-method             5.920  0.020   5.944
recurrentGenes-CopyNumberBreakPointGenes-method 5.888  0.016   5.908
* 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
  ‘/home/biocbuild/bbs-3.4-bioc/meat/GeneBreak.Rcheck/00check.log’
for details.


GeneBreak.Rcheck/00install.out:

* installing *source* package ‘GeneBreak’ ...
** R
** data
** inst
** preparing 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:

nameusersystemelapsed
CopyNumberBreakPointGenes-class7.6280.0647.701
CopyNumberBreakPoints-class1.7120.0241.736
accessOptions-CopyNumberBreakPoints-method0.9480.0040.952
addGeneAnnotation-CopyNumberBreakPoints-method2.4240.0082.434
bpFilter-CopyNumberBreakPoints-method1.1480.0121.161
bpGenes-CopyNumberBreakPointGenes-method2.7120.0242.736
bpPlot-CopyNumberBreakPoints-method5.9200.0205.944
bpStats-CopyNumberBreakPoints-method6.4200.0006.425
breakpointData-CopyNumberBreakPoints-method0.9800.1521.131
breakpointsPerGene-CopyNumberBreakPointGenes-method2.6640.1202.785
callData-CopyNumberBreakPoints-method1.0960.1281.225
featureChromosomes-CopyNumberBreakPoints-method0.8360.0160.853
featureInfo-CopyNumberBreakPoints-method2.5840.0402.628
featuresPerGene-CopyNumberBreakPointGenes-method2.4640.0162.480
geneChromosomes-CopyNumberBreakPointGenes-method2.6880.0122.702
geneInfo-CopyNumberBreakPointGenes-method2.320.022.34
getBreakpoints1.5800.0201.599
namesFeatures-CopyNumberBreakPoints-method0.8240.0080.834
recurrentGenes-CopyNumberBreakPointGenes-method5.8880.0165.908
sampleNames-CopyNumberBreakPoints-method0.8880.0000.889
segmentData-CopyNumberBreakPoints-method1.1040.1281.231