Back to the "Multiple platform build/check report" A  B  C  D  E  F  G  H  I  J  K  L [M] N  O  P  Q  R  S  T  U  V  W  X  Y  Z 

BioC 2.14: CHECK report for methylumi on zin2

This page was generated on 2014-10-08 08:48:38 -0700 (Wed, 08 Oct 2014).

Package 490/824HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
methylumi 2.10.0
Sean Davis
Snapshot Date: 2014-10-07 17:20:37 -0700 (Tue, 07 Oct 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_14/madman/Rpacks/methylumi
Last Changed Rev: 88838 / Revision: 95116
Last Changed Date: 2014-04-11 14:07:21 -0700 (Fri, 11 Apr 2014)
zin2 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK [ WARNINGS ]
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  WARNINGS  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  WARNINGS  OK 
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  WARNINGS  OK 

Summary

Package: methylumi
Version: 2.10.0
Command: /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings methylumi_2.10.0.tar.gz
StartedAt: 2014-10-08 01:00:45 -0700 (Wed, 08 Oct 2014)
EndedAt: 2014-10-08 01:04:29 -0700 (Wed, 08 Oct 2014)
EllapsedTime: 223.4 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: methylumi.Rcheck
Warnings: 3

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings methylumi_2.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-2.14-bioc/meat/methylumi.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘methylumi/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘methylumi’ version ‘2.10.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  ‘Biobase’ ‘scales’ ‘reshape2’ ‘ggplot2’ ‘matrixStats’ ‘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 for sufficient/correct file permissions ... OK
* checking whether package ‘methylumi’ can be installed ... [19s/19s] WARNING
Found the following significant warnings:
  Warning: replacing previous import by ‘graphics::image’ when loading ‘methylumi’
See ‘/home/biocbuild/bbs-2.14-bioc/meat/methylumi.Rcheck/00install.out’ for details.
* checking installed package size ... NOTE
  installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data      2.7Mb
    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
* 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:
  ‘ggplot2’ ‘matrixStats’ ‘minfi’ ‘reshape2’ ‘scales’
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘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.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* 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'
methylumIDAT: warning in gsub("_(Red|Grn)", "", barcodes, ignore =
  TRUE): partial argument match of 'ignore' to 'ignore.case'
methylumIDAT: warning in gsub(".idat", "", barcodes, ignore = TRUE):
  partial argument match of 'ignore' to 'ignore.case'
methylumIDAT2: warning in gsub("_(Red|Grn)", "", barcodes, ignore =
  TRUE): partial argument match of 'ignore' to 'ignore.case'
methylumIDAT2: warning in gsub(".idat", "", barcodes, ignore = TRUE):
  partial argument match of 'ignore' to 'ignore.case'
normexp.signal: warning in pnorm(0, mean = mu.sf, sd = sigma,
  lower.tail = FALSE, log = TRUE): partial argument match of 'log' to
  'log.p'
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 ‘chip’
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’
methylumi.diagnostics: no visible global function definition for
  ‘plot.density’
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 ‘withins’
normalizeViaSQN: no visible binding for global variable
  ‘normprobes.Cy3’
normalizeViaSQN: no visible binding for global variable
  ‘normprobes.Cy5’
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..’
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’
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’
* 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 S4 methods:
  generic '[' and siglist 'MethyLumiM,ANY'
  generic '[' and siglist 'MethyLumiSet,ANY'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See the chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... WARNING
Functions or methods with usage in documentation object 'methylumiMU' but not in code:
  methylumiMU

* 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 ... [13s/13s] 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

WARNING: There were 3 warnings.
NOTE: There were 6 notes.
See
  ‘/home/biocbuild/bbs-2.14-bioc/meat/methylumi.Rcheck/00check.log’
for details.

methylumi.Rcheck/00install.out:

* installing *source* package ‘methylumi’ ...
** R
** data
** inst
** preparing package for lazy loading
Warning: replacing previous import by ‘graphics::image’ when loading ‘methylumi’
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”
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import by ‘graphics::image’ when loading ‘methylumi’
* DONE (methylumi)

methylumi.Rcheck/methylumi-Ex.timings:

nameusersystemelapsed
CpGs1.5080.0121.524
MethyLumi-class0.6680.0160.685
MethyLumiM-class0.0040.0000.002
MethyLumiQC-class0.0000.0000.002
MethyLumiSet-class0.0000.0000.002
extractBarcodeAndPosition0.0080.0000.005
getAssayDataNameSubstitutions0.0040.0000.005
methylData-class0.0040.0000.001
methylumIDAT0.0000.0000.001
methylumiMU0.0040.0000.000
methylumiR0.3200.0040.326
mldat0.0640.0080.068
normalizeMethyLumiSet0.4680.0080.499
plotSampleIntensities0.0840.0000.086
qcplot0.2800.0000.281
varFilter0.5360.0000.535