Back to the "Multiple platform build/check report" A  B  C  D  E  F [G] H  I  J  K  L  M  N  O  P  Q  R  S  T  U  V  W  X  Y  Z 

BioC 3.4: CHECK report for GeneBreak on morelia

This page was generated on 2016-09-21 03:54:57 -0700 (Wed, 21 Sep 2016).

Package 466/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GeneBreak 1.3.0
Evert van den Broek
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GeneBreak
Last Changed Rev: 117081 / Revision: 121152
Last Changed Date: 2016-05-03 14:30:44 -0700 (Tue, 03 May 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / 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: 1.3.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings GeneBreak_1.3.0.tar.gz
StartedAt: 2016-09-20 06:55:02 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 06:57:51 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 169.2 seconds
RetCode: 0
Status:  OK 
CheckDir: GeneBreak.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings GeneBreak_1.3.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/GeneBreak.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.3.0’
* 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 sizes of PDF files under ‘inst/doc’ ... 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                 8.562  0.895   9.463
bpPlot-CopyNumberBreakPoints-method             6.561  0.741   7.303
bpStats-CopyNumberBreakPoints-method            5.976  0.894   6.869
recurrentGenes-CopyNumberBreakPointGenes-method 5.728  0.826   6.555
* 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-3.4-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-class8.5620.8959.463
CopyNumberBreakPoints-class1.8500.2382.091
accessOptions-CopyNumberBreakPoints-method1.3530.1311.485
addGeneAnnotation-CopyNumberBreakPoints-method3.1710.2013.375
bpFilter-CopyNumberBreakPoints-method1.8570.1892.046
bpGenes-CopyNumberBreakPointGenes-method2.6730.2312.903
bpPlot-CopyNumberBreakPoints-method6.5610.7417.303
bpStats-CopyNumberBreakPoints-method5.9760.8946.869
breakpointData-CopyNumberBreakPoints-method1.3510.3501.701
breakpointsPerGene-CopyNumberBreakPointGenes-method3.0620.5003.563
callData-CopyNumberBreakPoints-method1.3950.3581.754
featureChromosomes-CopyNumberBreakPoints-method1.0420.1271.170
featureInfo-CopyNumberBreakPoints-method2.6310.3252.955
featuresPerGene-CopyNumberBreakPointGenes-method2.6730.2672.942
geneChromosomes-CopyNumberBreakPointGenes-method2.4380.2612.699
geneInfo-CopyNumberBreakPointGenes-method2.5940.2612.855
getBreakpoints2.0600.1772.239
namesFeatures-CopyNumberBreakPoints-method0.9790.1241.103
recurrentGenes-CopyNumberBreakPointGenes-method5.7280.8266.555
sampleNames-CopyNumberBreakPoints-method1.1490.1451.294
segmentData-CopyNumberBreakPoints-method1.4010.3641.765