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Package 314/514HostnameOS / ArchBUILDCHECKBUILD BIN
methylumi 2.0.13
Sean Davis
Snapshot Date: 2012-03-23 18:21:46 -0700 (Fri, 23 Mar 2012)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_9/madman/Rpacks/methylumi
Last Changed Rev: 62597 / Revision: 64395
Last Changed Date: 2012-02-07 05:39:48 -0800 (Tue, 07 Feb 2012)
wilson2 Linux (openSUSE 11.4) / x86_64  OK  WARNINGS 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  WARNINGS  OK 
pitt Mac OS X Leopard (10.5.8) / i386  OK [ WARNINGS ] OK 

Summary

Package: methylumi
Version: 2.0.13
Command: /Library/Frameworks/R.framework/Versions/2.14/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch methylumi_2.0.13.tar.gz
StartedAt: 2012-03-24 02:30:45 -0700 (Sat, 24 Mar 2012)
EndedAt: 2012-03-24 02:33:35 -0700 (Sat, 24 Mar 2012)
EllapsedTime: 170.1 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: methylumi.Rcheck
Warnings: 2

Command output

* using log directory '/Users/biocbuild/bbs-2.9-bioc/meat/methylumi.Rcheck'
* using R version 2.14.2 (2012-02-29)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'methylumi/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'methylumi' version '2.0.13'
* 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 whether package 'methylumi' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data      2.7Mb
    extdata   1.7Mb
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... 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 namespace can be loaded with stated dependencies ... OK
* checking whether the namespace 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
compare.chips: no visible binding for global variable
  'IlluminaHumanMethylation450kCOLOR_CHANNEL'
compare.chips: no visible binding for global variable
  'IlluminaHumanMethylation27kCOLOR_CHANNEL'
compare.chips: no visible binding for global variable 'assay'
compare.chips: no visible binding for global variable 'chip'
compare.chips: no visible global function definition for
  'position_identity'
cy3: no visible global function definition for 'addColorChannelInfo'
cy5: no visible global function definition for 'addColorChannelInfo'
gamma.get.xcs: no visible global function definition for
  'gamma.integral'
gamma.get.xs : <anonymous>: no visible global function definition for
  'gamma.mle'
gamma.get.xs : <anonymous>: no visible global function definition for
  'gamma.integral'
gamma.signal: no visible global function definition for
  'gamma.integral'
gammaM.get.xs : <anonymous>: no visible global function definition for
  'gamma.mode'
gammaM.get.xs : <anonymous>: no visible global function definition for
  'gamma.mle'
normalize27kAnd450k: no visible binding for global variable
  'history.submitted'
normalizeViaSQN: no visible global function definition for
  'assayDataElements'
normalizeViaSQN: no visible binding for global variable 'CpGs'
normalizeViaSQN: no visible binding for global variable 'ctrl.id'
normalizeViaSQN: no visible binding for global variable 'subject'
normalizeViaSQN: no visible binding for global variable 'withins'
normalizeViaSQN: no visible binding for global variable
  'normprobes.Cy3'
normalizeViaSQN: no visible binding for global variable
  'normprobes.Cy5'
plotNegOob : <anonymous>: no visible global function definition for
  'melt'
plotNegOob: no visible binding for global variable 'intensity'
plotNegOob: no visible binding for global variable 'channel.probes'
plotNegOob: no visible binding for global variable '..density..'
plotNegOob: no visible global function definition for
  'position_identity'
qc.probe.plot: no visible global function definition for 'melt'
qc.probe.plot: no visible binding for global variable 'grouping'
qc.probe.plot: no visible binding for global variable 'variable'
qc.probe.plot: no visible binding for global variable 'value'
qc.probe.plot: no visible global function definition for 'scale_y_log2'
qc.probe.plot: no visible global function definition for 'scale_x_log2'
* checking Rd files ... NOTE
prepare_Rd: estimateM.Rd:34-36: Dropping empty section \seealso
prepare_Rd: estimateM.Rd:37-39: Dropping empty section \examples
prepare_Rd: methylumIDAT.Rd:53-55: Dropping empty section \seealso
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  'IDATsToMatrices' 'IDATtoMatrix'
Undocumented data sets:
  'CpGs'
All user-level objects in a package should have documentation entries.
See the chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'methylumIDAT':
methylumIDAT
  Code: function(barcodes = NULL, pdat = NULL, parallel = F, n = F,
                 n.sd = F, oob = T, idatPath = getwd(), with.hg18 =
                 FALSE, ...)
  Docs: function(barcodes = NULL, pdat = NULL, parallel = F, n = T,
                 n.sd = F, oob = T, idatPath = getwd(), ...)
  Argument names in code not in docs:
    with.hg18
  Mismatches in argument names:
    Position: 8 Code: with.hg18 Docs: ...
  Mismatches in argument default values:
    Name: 'n' Code: F Docs: T

* 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 examples ... OK
* 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

WARNING: There were 2 warnings, see
  '/Users/biocbuild/bbs-2.9-bioc/meat/methylumi.Rcheck/00check.log'
for details

methylumi.Rcheck/00install.out:

* installing *source* package 'methylumi' ...
** R
** data
** inst
** preparing package for lazy loading
in method for 'total.intensity' with signature 'object="MethyLumiSet"': no definition for class "MethyLumiSet"
in method for 'total.intensity' with signature 'object="MethyLumiM"': no definition for class "MethyLumiM"
in method for 'intensitiesByChannel' with signature 'object="MethyLumiSet"': no definition for class "MethyLumiSet"
in method for 'intensitiesByChannel' with signature 'object="MethyLumiM"': no definition for class "MethyLumiM"
in method for 'Cy3.SD' with signature 'object="MethyLumiSet"': no definition for class "MethyLumiSet"
in method for 'Cy3.N' with signature 'object="MethyLumiSet"': no definition for class "MethyLumiSet"
in method for 'Cy5.SD' with signature 'object="MethyLumiSet"': no definition for class "MethyLumiSet"
in method for 'Cy5.N' with signature 'object="MethyLumiSet"': no definition for class "MethyLumiSet"
in method for 'negctls' with signature 'object="MethyLumiSet",channel="character"': no definition for class "MethyLumiSet"
in method for 'negctls' with signature 'object="MethyLumiSet",channel="missing"': no definition for class "MethyLumiSet"
in method for 'negctls' with signature 'object="MethyLumiM",channel="character"': no definition for class "MethyLumiM"
in method for 'negctls' with signature 'object="MethyLumiM",channel="missing"': no definition for class "MethyLumiM"
in method for 'negctls.SD' with signature 'object="MethyLumiSet",channel="character"': no definition for class "MethyLumiSet"
in method for 'negctls.SD' with signature 'object="MethyLumiM",channel="character"': no definition for class "MethyLumiM"
in method for 'negctls.stderr' with signature 'object="MethyLumiSet",channel="character"': no definition for class "MethyLumiSet"
in method for 'negctls.stderr' with signature 'object="MethyLumiSet",channel="missing"': no definition for class "MethyLumiSet"
in method for 'negnorm' with signature 'object="MethyLumiSet",channel="character"': no definition for class "MethyLumiSet"
in method for 'negnorm' with signature 'object="MethyLumiM",channel="character"': no definition for class "MethyLumiM"
in method for 'negnorm' with signature 'object="MethyLumiSet",channel="missing"': no definition for class "MethyLumiSet"
in method for 'negnorm' with signature 'object="MethyLumiM",channel="missing"': no definition for class "MethyLumiM"
in method for 'normctls' with signature 'object="MethyLumiSet"': no definition for class "MethyLumiSet"
in method for 'normctls' with signature 'object="MethyLumiM"': no definition for class "MethyLumiM"
Creating a generic function for 'summary' from package 'base' in package 'methylumi'
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   'methylumi.Rnw' 
** testing if installed package can be loaded

* DONE (methylumi)

methylumi.Rcheck/methylumi-Ex.timings:

nameusersystemelapsed
MethyLumi-class1.0270.0431.088
MethyLumiM-class0.0020.0010.002
MethyLumiQC-class0.0010.0000.002
MethyLumiSet-class0.0020.0000.002
extractBarcodeAndPosition0.0050.0010.007
getAssayDataNameSubstitutions0.0050.0020.006
methylData-class0.0010.0000.001
methylumIDAT000
methylumiR0.7180.0270.760
mldat0.2010.0110.212
normalizeMethyLumiSet1.1880.0351.250
plotSampleIntensities0.1920.0080.204
qcplot0.5060.0110.529
varFilter1.0070.0221.039