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BioC 3.1: CHECK report for methylumi on moscato2

This page was generated on 2015-10-09 09:28:33 -0700 (Fri, 09 Oct 2015).

Package 594/1024HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
methylumi 2.14.0
Sean Davis
Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/methylumi
Last Changed Rev: 102591 / Revision: 109384
Last Changed Date: 2015-04-16 12:42:01 -0700 (Thu, 16 Apr 2015)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: methylumi
Version: 2.14.0
Command: rm -rf methylumi.buildbin-libdir methylumi.Rcheck && mkdir methylumi.buildbin-libdir methylumi.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=methylumi.buildbin-libdir methylumi_2.14.0.tar.gz >methylumi.Rcheck\00install.out 2>&1 && cp methylumi.Rcheck\00install.out methylumi-install.out && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=methylumi.buildbin-libdir --install="check:methylumi-install.out" --force-multiarch --no-vignettes --timings methylumi_2.14.0.tar.gz
StartedAt: 2015-10-09 03:43:52 -0700 (Fri, 09 Oct 2015)
EndedAt: 2015-10-09 03:49:51 -0700 (Fri, 09 Oct 2015)
EllapsedTime: 358.6 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: methylumi.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf methylumi.buildbin-libdir methylumi.Rcheck && mkdir methylumi.buildbin-libdir methylumi.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=methylumi.buildbin-libdir methylumi_2.14.0.tar.gz >methylumi.Rcheck\00install.out 2>&1 && cp methylumi.Rcheck\00install.out methylumi-install.out  && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=methylumi.buildbin-libdir --install="check:methylumi-install.out" --force-multiarch --no-vignettes --timings methylumi_2.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbld/bbs-3.1-bioc/meat/methylumi.Rcheck'
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-w64-mingw32 (64-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 '2.14.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'Biobase' 'scales' 'reshape2' 'ggplot2' 'matrixStats'
  'FDb.InfiniumMethylation.hg19' 'minfi'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 'methylumi' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  9.6Mb
  sub-directories of 1Mb or more:
    data      6.8Mb
    extdata   1.7Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  'Biobase' 'minfi' 'lattice' 'matrixStats'
A package should be listed in only one of these fields.
* 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
* 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 dependencies in R code ... NOTE
'library' or 'require' calls to packages already attached by Depends:
  'FDb.InfiniumMethylation.hg19' 'ggplot2' 'matrixStats' 'minfi'
  'reshape2' 'scales'
  Please remove these calls from your code.
'library' or 'require' calls in package code:
  'Biostrings' 'MASS' 'lumi' 'parallel' 'rtracklayer'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Namespace in Imports field not imported from: 'graphics'
  All declared Imports should be used.
Packages in Depends field not imported from:
  'FDb.InfiniumMethylation.hg19' 'ggplot2' 'matrixStats' 'methods'
  'reshape2' 'scales'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
':::' call which should be '::': 'lumi:::produceMethylationGEOSubmissionFile'
  See the note in ?`:::` about the use of this operator.
Unexported objects imported by ':::' calls:
  'Biobase:::unsafeSetSlot' 'genefilter:::.findCentralMap'
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
getBarcodes: warning in list.files(path = path, patt = "idat"): partial
  argument match of 'patt' to 'pattern'
normexp.signal: warning in pnorm(0, mean = mu.sf, sd = sigma,
  lower.tail = FALSE, log = TRUE): partial argument match of 'log' to
  'log.p'
.mclapply: no visible global function definition for 'mclapply'
SEtoGRset: no visible global function definition for 'GenomicRatioSet'
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'
getMethylationBeadMappers : <anonymous>: no visible binding for global
  variable 'hm27.controls'
getMethylationBeadMappers : <anonymous>: no visible binding for global
  variable 'hm450.controls'
getMethylationBeadMappers : <anonymous>: no visible binding for global
  variable 'hm27.ordering'
getMethylationBeadMappers : <anonymous>: no visible binding for global
  variable 'hm450.ordering'
getPlatform: no visible global function definition for 'features'
getPlatform: no visible binding for global variable
  'FDb.InfiniumMethylation.hg19'
getPlatform: no visible global function definition for 'DNAStringSet'
illumina.get.xs: no visible global function definition for
  'colQuantiles'
median.get.xs: no visible global function definition for 'colMedians'
methylumi.bgcorr: no visible binding for global variable
  'IlluminaHumanMethylation27kCOLORCHANNEL'
methylumi.bgcorr: no visible binding for global variable
  'IlluminaHumanMethylation450kCOLORCHANNEL'
methylumi.diagnostics: no visible binding for global variable
  'IlluminaHumanMethylation27kCOLORCHANNEL'
methylumi.diagnostics: no visible binding for global variable
  'IlluminaHumanMethylation450kCOLORCHANNEL'
methylumi.diagnostics: no visible global function definition for
  'plot.density'
methylumiCSV: no visible global function definition for
  'DFsToNChannelSet'
methylumiToMinfi: no visible global function definition for
  'RGChannelSet'
normexp.get.xs: no visible global function definition for 'huber'
normexp.get.xs: no visible global function definition for 'colSds'
plotNegOob : <anonymous>: no visible global function definition for
  'melt'
plotNegOob: no visible global function definition for 'ggplot'
plotNegOob: no visible global function definition for 'aes'
plotNegOob: no visible binding for global variable 'intensity'
plotNegOob: no visible binding for global variable 'channel.probes'
plotNegOob: no visible global function definition for 'geom_histogram'
plotNegOob: no visible binding for global variable '..density..'
plotNegOob: no visible global function definition for
  'position_identity'
plotNegOob: no visible global function definition for 'facet_grid'
plotNegOob: no visible global function definition for
  'scale_x_continuous'
plotNegOob: no visible global function definition for
  'scale_y_continuous'
plotNegOob: no visible global function definition for
  'scale_fill_manual'
plotNegOob: no visible global function definition for 'opts'
plotNegOob: no visible global function definition for 'theme_bw'
qc.probe.plot: no visible global function definition for 'log_trans'
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 'coord_flip'
qc.probe.plot: no visible global function definition for
  'scale_x_continuous'
qc.probe.plot: no visible global function definition for
  'scale_y_discrete'
qc.probe.plot: no visible global function definition for 'facet_grid'
qc.probe.plot: no visible global function definition for
  'scale_colour_manual'
qc.probe.plot: no visible global function definition for
  'scale_shape_manual'
qc.probe.plot: no visible global function definition for 'theme_bw'
coerce,MethyLumiM-MethylSet: no visible global function definition for
  'MethylSet'
coerce,MethyLumiSet-MethylSet: no visible global function definition
  for 'MethylSet'
coerce,SummarizedExperiment-GenomicMethylSet: no visible global
  function definition for 'GenomicMethylSet'
combine27k450k,MethyLumiSet-MethyLumiSet : .local: no visible global
  function definition for 'subsetCommonProbes'
getProbesByChannel,methylData : .local : <anonymous>: no visible
  binding for global variable 'allele'
initialize,MethyLumiQC : .local: ... may be used in an incorrect
  context: 'assayDataNew(...)'
intensities.IB,MethyLumiSet-character: no visible binding for global
  variable 'IlluminaHumanMethylation27kCOLORCHANNEL'
intensities.IB,MethyLumiSet-character: no visible binding for global
  variable 'IlluminaHumanMethylation450kCOLORCHANNEL'
intensities.M,MethyLumiSet-character: no visible binding for global
  variable 'IlluminaHumanMethylation27kCOLORCHANNEL'
intensities.M,MethyLumiSet-character: no visible binding for global
  variable 'IlluminaHumanMethylation450kCOLORCHANNEL'
intensities.OOB.allelic,MethyLumiSet-character-character: no visible
  binding for global variable 'IlluminaHumanMethylation27kCOLORCHANNEL'
intensities.OOB.allelic,MethyLumiSet-character-character: no visible
  binding for global variable
  'IlluminaHumanMethylation450kCOLORCHANNEL'
intensities.OOB,MethyLumiSet-character: no visible binding for global
  variable 'IlluminaHumanMethylation27kCOLORCHANNEL'
intensities.OOB,MethyLumiSet-character: no visible binding for global
  variable 'IlluminaHumanMethylation450kCOLORCHANNEL'
intensities.U,MethyLumiSet-character: no visible binding for global
  variable 'IlluminaHumanMethylation27kCOLORCHANNEL'
intensities.U,MethyLumiSet-character: no visible binding for global
  variable 'IlluminaHumanMethylation450kCOLORCHANNEL'
plotNAs,methylData: no visible binding for global variable 'index'
plotNAs,methylData: no visible binding for global variable 'dropouts'
plotProbeNAs,methylData: no visible binding for global variable 'mu'
plotProbeNAs,methylData: no visible binding for global variable 'drops'
pval.detect<-,methylData-numeric: no visible global function definition
  for 'rowMins'
* 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:52-54: Dropping empty section \seealso
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  'IDATsToMatrices' 'IDATtoMatrix' 'tcgaPipeline'
Undocumented data sets:
  'mset'
Undocumented S4 methods:
  generic '[' and siglist 'MethyLumiM,ANY,ANY'
  generic '[' and siglist 'MethyLumiSet,ANY,ANY'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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' ... [16s] OK
** running examples for arch 'x64' ... [18s] 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 6 NOTEs
See
  'E:/biocbld/bbs-3.1-bioc/meat/methylumi.Rcheck/00check.log'
for details.


methylumi.Rcheck/00install.out:


install for i386

* installing *source* package 'methylumi' ...
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'

install for x64

* installing *source* package 'methylumi' ...
** testing if installed package can be loaded
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
* MD5 sums
packaged installation of 'methylumi' as methylumi_2.14.0.zip
* DONE (methylumi)

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

nameusersystemelapsed
CpGs1.130.011.14
MethyLumi-class0.920.000.92
MethyLumiM-class000
MethyLumiQC-class000
MethyLumiSet-class000
extractBarcodeAndPosition0.020.000.01
getAssayDataNameSubstitutions000
methylData-class000
methylumIDAT000
methylumiR0.450.000.45
mldat0.110.020.13
normalizeMethyLumiSet0.710.000.70
plotSampleIntensities0.100.010.12
qcplot0.290.000.28
varFilter0.490.020.52

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

nameusersystemelapsed
CpGs1.700.021.72
MethyLumi-class1.450.031.48
MethyLumiM-class000
MethyLumiQC-class0.020.000.02
MethyLumiSet-class000
extractBarcodeAndPosition000
getAssayDataNameSubstitutions0.010.000.01
methylData-class000
methylumIDAT000
methylumiR0.410.030.44
mldat0.110.000.11
normalizeMethyLumiSet0.560.020.58
plotSampleIntensities0.090.000.09
qcplot0.300.010.31
varFilter0.560.000.56