Package: methylumi

Version: 2.0.13

Command: rm -rf methylumi.buildbin-libdir && mkdir methylumi.buildbin-libdir && D:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=methylumi.buildbin-libdir methylumi_2.0.13.tar.gz >methylumi-install.out 2>&1 && D:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD check --library=methylumi.buildbin-libdir --install="check:methylumi-install.out" --force-multiarch --no-vignettes --timings methylumi_2.0.13.tar.gz && mv methylumi.buildbin-libdir/* methylumi.Rcheck/ && rmdir methylumi.buildbin-libdir

StartedAt: 2012-03-24 02:05:56 -0700 (Sat, 24 Mar 2012)

EndedAt: 2012-03-24 02:08:42 -0700 (Sat, 24 Mar 2012)

EllapsedTime: 165.5 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: methylumi.Rcheck

Warnings: 2

* using log directory 'D:/biocbld/bbs-2.9-bioc/meat/methylumi.Rcheck'
* using R version 2.14.2 (2012-02-29)
* using platform: i386-pc-mingw32 (32-bit)
* using session charset: ISO8859-1
* 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 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
* 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
* 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 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 examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... 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
  'D:/biocbld/bbs-2.9-bioc/meat/methylumi.Rcheck/00check.log'
for details

install for i386

* 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

add DLL for x64

* installing *source* package 'methylumi' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'methylumi' as methylumi_2.0.13.zip

* DONE (methylumi)