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BioC 3.5: CHECK report for GeneBreak on tokay2

This page was generated on 2017-08-16 13:25:03 -0400 (Wed, 16 Aug 2017).

Package 508/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GeneBreak 1.6.0
Evert van den Broek
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/GeneBreak
Last Changed Rev: 129126 / Revision: 131943
Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: GeneBreak
Version: 1.6.0
Command: rm -rf GeneBreak.buildbin-libdir GeneBreak.Rcheck && mkdir GeneBreak.buildbin-libdir GeneBreak.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GeneBreak.buildbin-libdir GeneBreak_1.6.0.tar.gz >GeneBreak.Rcheck\00install.out 2>&1 && cp GeneBreak.Rcheck\00install.out GeneBreak-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=GeneBreak.buildbin-libdir --install="check:GeneBreak-install.out" --force-multiarch --no-vignettes --timings GeneBreak_1.6.0.tar.gz
StartedAt: 2017-08-15 23:54:56 -0400 (Tue, 15 Aug 2017)
EndedAt: 2017-08-16 00:00:06 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 310.0 seconds
RetCode: 0
Status:  OK  
CheckDir: GeneBreak.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf GeneBreak.buildbin-libdir GeneBreak.Rcheck && mkdir GeneBreak.buildbin-libdir GeneBreak.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GeneBreak.buildbin-libdir GeneBreak_1.6.0.tar.gz >GeneBreak.Rcheck\00install.out 2>&1 && cp GeneBreak.Rcheck\00install.out GeneBreak-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=GeneBreak.buildbin-libdir --install="check:GeneBreak-install.out" --force-multiarch --no-vignettes --timings GeneBreak_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/GeneBreak.Rcheck'
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'GeneBreak/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'GeneBreak' version '1.6.0'
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                                                user system elapsed
CopyNumberBreakPointGenes-class                 8.70   0.28    8.99
bpStats-CopyNumberBreakPoints-method            7.06   0.19    7.25
bpPlot-CopyNumberBreakPoints-method             6.90   0.21    7.11
recurrentGenes-CopyNumberBreakPointGenes-method 6.31   0.26    6.57
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                                                user system elapsed
CopyNumberBreakPointGenes-class                 8.28   0.30    8.58
bpStats-CopyNumberBreakPoints-method            7.47   0.17    7.64
recurrentGenes-CopyNumberBreakPointGenes-method 7.01   0.29    7.33
bpPlot-CopyNumberBreakPoints-method             6.59   0.10    6.70
* 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
  'C:/Users/biocbuild/bbs-3.5-bioc/meat/GeneBreak.Rcheck/00check.log'
for details.


GeneBreak.Rcheck/00install.out:


install for i386

* 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

install for x64

* installing *source* package 'GeneBreak' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GeneBreak' as GeneBreak_1.6.0.zip
* DONE (GeneBreak)

GeneBreak.Rcheck/examples_i386/GeneBreak-Ex.timings:

nameusersystemelapsed
CopyNumberBreakPointGenes-class8.700.288.99
CopyNumberBreakPoints-class2.190.142.32
accessOptions-CopyNumberBreakPoints-method0.970.141.11
addGeneAnnotation-CopyNumberBreakPoints-method2.910.213.11
bpFilter-CopyNumberBreakPoints-method1.390.261.66
bpGenes-CopyNumberBreakPointGenes-method2.970.173.14
bpPlot-CopyNumberBreakPoints-method6.900.217.11
bpStats-CopyNumberBreakPoints-method7.060.197.25
breakpointData-CopyNumberBreakPoints-method1.160.291.45
breakpointsPerGene-CopyNumberBreakPointGenes-method3.470.253.72
callData-CopyNumberBreakPoints-method1.480.391.88
featureChromosomes-CopyNumberBreakPoints-method0.960.081.03
featureInfo-CopyNumberBreakPoints-method3.430.173.61
featuresPerGene-CopyNumberBreakPointGenes-method3.300.113.40
geneChromosomes-CopyNumberBreakPointGenes-method3.080.213.28
geneInfo-CopyNumberBreakPointGenes-method2.800.213.02
getBreakpoints2.010.192.20
namesFeatures-CopyNumberBreakPoints-method1.050.031.08
recurrentGenes-CopyNumberBreakPointGenes-method6.310.266.57
sampleNames-CopyNumberBreakPoints-method0.800.130.93
segmentData-CopyNumberBreakPoints-method1.360.311.67

GeneBreak.Rcheck/examples_x64/GeneBreak-Ex.timings:

nameusersystemelapsed
CopyNumberBreakPointGenes-class8.280.308.58
CopyNumberBreakPoints-class1.620.251.88
accessOptions-CopyNumberBreakPoints-method1.260.121.39
addGeneAnnotation-CopyNumberBreakPoints-method2.710.222.93
bpFilter-CopyNumberBreakPoints-method1.710.271.98
bpGenes-CopyNumberBreakPointGenes-method2.930.223.14
bpPlot-CopyNumberBreakPoints-method6.590.106.70
bpStats-CopyNumberBreakPoints-method7.470.177.64
breakpointData-CopyNumberBreakPoints-method1.860.352.20
breakpointsPerGene-CopyNumberBreakPointGenes-method3.140.323.47
callData-CopyNumberBreakPoints-method1.420.221.64
featureChromosomes-CopyNumberBreakPoints-method1.200.141.34
featureInfo-CopyNumberBreakPoints-method3.430.203.63
featuresPerGene-CopyNumberBreakPointGenes-method2.870.143.01
geneChromosomes-CopyNumberBreakPointGenes-method3.050.253.32
geneInfo-CopyNumberBreakPointGenes-method3.000.253.26
getBreakpoints2.190.162.34
namesFeatures-CopyNumberBreakPoints-method1.030.141.18
recurrentGenes-CopyNumberBreakPointGenes-method7.010.297.33
sampleNames-CopyNumberBreakPoints-method1.170.081.27
segmentData-CopyNumberBreakPoints-method1.070.221.28