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Package 322/419HostnameOS / ArchBUILDCHECKBUILD BIN
R453Plus1Toolbox 1.0.1
H-U Klein
Snapshot Date: 2011-04-06 23:24:01 -0700 (Wed, 06 Apr 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_7/madman/Rpacks/R453Plus1Toolbox
Last Changed Rev: 50365 / Revision: 54588
Last Changed Date: 2010-10-20 09:22:14 -0700 (Wed, 20 Oct 2010)
lamb2 Linux (openSUSE 11.2) / x86_64  OK  OK 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK  OK  OK 
gewurz Windows Server 2008 R2 Enterprise (64-bit) / x64  OK [ OK ] OK 

Summary

Package: R453Plus1Toolbox
Version: 1.0.1
Command: D:\biocbld\bbs-2.7-bioc\R\bin\R.exe CMD check --no-vignettes --timings R453Plus1Toolbox_1.0.1.tar.gz
StartedAt: 2011-04-07 12:31:41 -0700 (Thu, 07 Apr 2011)
EndedAt: 2011-04-07 12:36:20 -0700 (Thu, 07 Apr 2011)
EllapsedTime: 279.2 seconds
RetCode: 0
Status:  OK  
CheckDir: R453Plus1Toolbox.Rcheck
Warnings: 0

Command output

* using log directory 'D:/biocbld/bbs-2.7-bioc/meat/R453Plus1Toolbox.Rcheck'
* using R version 2.12.2 (2011-02-25)
* using platform: x86_64-pc-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'R453Plus1Toolbox/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'R453Plus1Toolbox' version '1.0.1'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'R453Plus1Toolbox' can be installed ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level 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 name space can be loaded with stated dependencies ... OK
* checking whether the name space can be unloaded cleanly ... OK
* checking for unstated 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
.getMutations: no visible binding for global variable 'PatternStart'
.getMutations: no visible binding for global variable 'PatternEnd'
.htmlReport: no visible binding for global variable 'VarFreqForward'
.htmlReport: no visible binding for global variable 'VarFreqReverse'
* 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 data for non-ASCII characters ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... SKIPPED
* checking PDF version of manual ... OK

R453Plus1Toolbox.Rcheck/00install.out:

* installing *source* package 'R453Plus1Toolbox' ...
** R
** data
** inst
** preparing package for lazy loading

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'openVignette()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation(pkgname)'.

Loading required package: IRanges

Attaching package: 'IRanges'

The following object(s) are masked from 'package:Biobase':

    updateObject

The following object(s) are masked from 'package:base':

    Map, cbind, eval, mapply, order, paste, pmax, pmax.int, pmin,
    pmin.int, rbind, rep.int, table

Loading required package: BSgenome
Loading required package: GenomicRanges
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (R453Plus1Toolbox)

R453Plus1Toolbox.Rcheck/R453Plus1Toolbox-Ex.timings:

nameusersystemelapsed
AVASet-class0.290.020.32
AVASet0.020.000.01
AnnotatedVariants-class0.020.000.02
MapperSet-class0.040.000.04
MapperSet000
alignShortReads0.960.011.13
annotateVariants0.010.000.01
assayDataAmp000
avaSetExample0.030.000.04
avaSetFiltered0.050.000.04
avaSetFiltered_annot0.010.000.02
breakpoints000
captureArray0.020.000.01
coverageOnTarget0.420.000.55
demultiplexReads0.350.020.67
detectBreakpoints0.760.010.89
fDataAmp0.030.000.03
featureDataAmp0.030.000.04
filterChimericReads1.690.001.68
genomeSequencerMIDs0.060.000.07
getAlignedReads0.180.000.17
getVariantPercentages0.060.000.07
htmlReport4.640.325.40
mapperSetExample0.020.000.02
mergeBreakpoints7.890.238.15
plotAmpliconCoverage000
plotChimericReads5.380.005.39
plotVariants000
plotVariationFrequency000
readsOnTarget0.470.000.47
referenceSequences0.020.000.01
removeLinker0.030.000.04
sequenceCaptureLinkers000
setVariantFilter0.110.000.11
transcriptdf0.020.000.02