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BioC 3.0: CHECK report for wateRmelon on oaxaca

This page was generated on 2015-04-10 10:06:40 -0700 (Fri, 10 Apr 2015).

Package 921/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
wateRmelon 1.6.0
Leo
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/wateRmelon
Last Changed Rev: 97632 / Revision: 102249
Last Changed Date: 2014-12-14 01:12:54 -0800 (Sun, 14 Dec 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK  WARNINGS 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  WARNINGS  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  WARNINGS  OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK [ WARNINGS ] OK 

Summary

Package: wateRmelon
Version: 1.6.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch wateRmelon_1.6.0.tar.gz
StartedAt: 2015-04-10 04:06:18 -0700 (Fri, 10 Apr 2015)
EndedAt: 2015-04-10 04:13:03 -0700 (Fri, 10 Apr 2015)
EllapsedTime: 405.3 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: wateRmelon.Rcheck
Warnings: 3

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch wateRmelon_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/wateRmelon.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘wateRmelon/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘wateRmelon’ version ‘1.6.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: ‘IMA’

Depends: includes the non-default packages:
  ‘limma’ ‘matrixStats’ ‘methylumi’ ‘lumi’ ‘ROC’
  ‘IlluminaHumanMethylation450kanno.ilmn12.hg19’
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 ‘wateRmelon’ can be installed ... [43s/43s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘methylumi’
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 ... WARNING
Invalid citation information in ‘inst/CITATION’:
  Error in parse(file = cfile): /Users/biocbuild/bbs-3.0-bioc/meat/wateRmelon.Rcheck/00_pkg_src/wateRmelon/inst/CITATION:4:1: unexpected '/'
  3:         doi = "10.1186/1471-2164-14-293",
  4: /
     ^
* 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' call to ‘methylumi’ which was already attached by Depends.
  Please remove these calls from your code.
'library' or 'require' calls in package code:
  ‘IMA’ ‘minfi’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  ‘IlluminaHumanMethylation450kanno.ilmn12.hg19’ ‘ROC’ ‘limma’ ‘lumi’
  ‘matrixStats’ ‘methods’ ‘methylumi’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
beadcount: no visible global function definition for ‘assayDataElement’
beadcount: no visible global function definition for ‘getProbeInfo’
beadcount: no visible global function definition for ‘getManifestInfo’
beadcount: no visible global function definition for ‘sampleNames’
bgIntensitySwan.methylumi: no visible global function definition for
  ‘colMedians’
combo: no visible binding for global variable ‘assayData’
combo: no visible binding for global variable ‘pData’
combo: no visible binding for global variable ‘protocolData’
combo: no visible binding for global variable ‘experimentData’
combo : <anonymous>: no visible global function definition for
  ‘assayData’
combo : <anonymous>: no visible global function definition for ‘QCdata’
combo: no visible global function definition for ‘assayData<-’
combo: no visible global function definition for ‘pData<-’
combo: no visible global function definition for ‘protocolData<-’
combo: no visible global function definition for ‘experimentData<-’
combo: no visible global function definition for ‘QCdata<-’
combo: no visible global function definition for ‘fData<-’
combo: no visible global function definition for ‘fData’
combo: no visible global function definition for ‘annotation<-’
combo: no visible global function definition for ‘annotation’
db1: no visible global function definition for ‘normalizeQuantiles’
detectionPval.filter: no visible global function definition for
  ‘assayDataElement’
dfort: no visible binding for global variable
  ‘IlluminaHumanMethylation450kanno.ilmn12.hg19’
filterXY: no visible global function definition for ‘fData’
filterXY: no visible global function definition for ‘featureNames’
genall: no visible global function definition for ‘featureNames’
genall: no visible global function definition for ‘betas’
getMethylumiBeta: no visible global function definition for
  ‘featureNames’
getMethylumiBeta: no visible global function definition for
  ‘unmethylated’
getMethylumiBeta: no visible global function definition for
  ‘methylated’
getSamples: no visible global function definition for ‘sampleNames’
got: no visible global function definition for ‘getProbeInfo’
loadMethylumi2: no visible global function definition for
  ‘addControlData2methyLumiM’
lumiMethyR2: no visible global function definition for ‘methylumiR’
lumiMethyR2: no visible global function definition for ‘sampleNames’
lumiMethyR2: no visible global function definition for
  ‘assayDataElement<-’
lumiMethyR2: no visible global function definition for
  ‘assayDataElement’
lumiMethyR2: no visible global function definition for
  ‘addAnnotationInfo’
lumiMethyR2: no visible global function definition for ‘controlData<-’
nbBeadsFilter: no visible global function definition for
  ‘assayDataElement’
nbBeadsFilter: no visible global function definition for
  ‘assayDataElement<-’
pipelineIlluminaMethylation.batch: possible error in
  preprocessIlluminaMethylation(path2data = path2data, path2controlData
  = path2controlData, projectName = projectName, nbBeads.threshold =
  nbBeads.threshold, detectionPval.threshold = detectionPval.threshold,
  detectionPval.perc.threshold = detectionPval.perc.threshold,
  sample2keep = path2sampleList, probeSNP_LIST, XY.filtering =
  XY.filtering, colorBias.corr = colorBias.corr, bg.adjust = bg.adjust,
  PATH = PATH_RES): unused arguments (path2data = path2data,
  path2controlData = path2controlData, projectName = projectName)
pipelineIlluminaMethylation.batch: no visible binding for global
  variable ‘PATH_RES’
pipelineIlluminaMethylation.batch: no visible global function
  definition for ‘assayDataElement’
pipelineIlluminaMethylation.batch: no visible global function
  definition for ‘fData’
pipelineIlluminaMethylation.batch: no visible binding for global
  variable ‘probeAnnotationsCategory’
preprocessIlluminaMethylation: no visible binding for global variable
  ‘projectName’
preprocessIlluminaMethylation: no visible global function definition
  for ‘sampleNames’
preprocessIlluminaMethylation: no visible global function definition
  for ‘featureNames’
preprocessIlluminaMethylation: no visible global function definition
  for ‘lumiMethyB’
seabird: no visible global function definition for ‘pAUC’
seabird: no visible global function definition for ‘rocdemo.sca’
betaqn,MethyLumiSet: no visible global function definition for
  ‘betas<-’
betaqn,MethyLumiSet: no visible global function definition for ‘betas’
betaqn,MethylSet: no visible global function definition for ‘getBeta’
betaqn,RGChannelSet: no visible global function definition for
  ‘getBeta’
colnames,MethyLumiSet: no visible global function definition for
  ‘methylated’
danen,MethyLumiSet: no visible global function definition for
  ‘methylated’
danen,MethyLumiSet: no visible global function definition for
  ‘unmethylated’
danen,MethyLumiSet: no visible global function definition for ‘betas<-’
danen,MethyLumiSet: no visible global function definition for
  ‘methylated<-’
danen,MethyLumiSet: no visible global function definition for
  ‘unmethylated<-’
danen,MethylSet: no visible global function definition for ‘getMeth’
danen,MethylSet: no visible global function definition for ‘getUnmeth’
danen,RGChannelSet: no visible global function definition for
  ‘preprocessRaw’
danes,MethyLumiSet: no visible global function definition for
  ‘methylated’
danes,MethyLumiSet: no visible global function definition for
  ‘unmethylated’
danes,MethyLumiSet: no visible global function definition for ‘betas<-’
danes,MethyLumiSet: no visible global function definition for
  ‘methylated<-’
danes,MethyLumiSet: no visible global function definition for
  ‘unmethylated<-’
danet,MethyLumiSet: no visible global function definition for
  ‘methylated’
danet,MethyLumiSet: no visible global function definition for
  ‘unmethylated’
danet,MethyLumiSet: no visible global function definition for ‘betas<-’
danet,MethyLumiSet: no visible global function definition for
  ‘methylated<-’
danet,MethyLumiSet: no visible global function definition for
  ‘unmethylated<-’
daten1,MethyLumiSet: no visible global function definition for
  ‘methylated’
daten1,MethyLumiSet: no visible global function definition for
  ‘unmethylated’
daten1,MethyLumiSet: no visible global function definition for
  ‘betas<-’
daten1,MethyLumiSet: no visible global function definition for
  ‘methylated<-’
daten1,MethyLumiSet: no visible global function definition for
  ‘unmethylated<-’
daten1,MethylSet: no visible global function definition for ‘getMeth’
daten1,MethylSet: no visible global function definition for ‘getUnmeth’
daten1,RGChannelSet: no visible global function definition for
  ‘preprocessRaw’
daten2,MethyLumiSet: no visible global function definition for
  ‘methylated’
daten2,MethyLumiSet: no visible global function definition for
  ‘unmethylated’
daten2,MethyLumiSet: no visible global function definition for
  ‘betas<-’
daten2,MethyLumiSet: no visible global function definition for
  ‘methylated<-’
daten2,MethyLumiSet: no visible global function definition for
  ‘unmethylated<-’
daten2,MethylSet: no visible global function definition for ‘getMeth’
daten2,MethylSet: no visible global function definition for ‘getUnmeth’
dmrse,MethylSet: no visible global function definition for ‘getBeta’
dmrse,RGChannelSet: no visible global function definition for ‘getBeta’
dmrse_col,MethylSet: no visible global function definition for
  ‘getBeta’
dmrse_col,RGChannelSet: no visible global function definition for
  ‘getBeta’
dmrse_row,MethylSet: no visible global function definition for
  ‘getBeta’
dmrse_row,RGChannelSet: no visible global function definition for
  ‘getBeta’
seabi,MethyLumiSet: no visible global function definition for ‘betas’
seabi,MethylSet: no visible global function definition for ‘getBeta’
seabi,RGChannelSet: no visible global function definition for ‘getBeta’
seabi,exprmethy450: no visible binding for global variable ‘object’
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘anSNP’ ‘aoget’ ‘dfort’ ‘genall’ ‘genme’ ‘genus’ ‘goodSNP’ ‘qual’
All user-level objects in a package should have documentation entries.
See 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 'got' but not in code:
  pop

Codoc mismatches from documentation object 'dasen':
danes
  Code: function(mn, un, onetwo, fudge = 100, ret2 = FALSE, ...)
  Docs: function(mn, un, onetwo, fudge = 100, ...)
  Argument names in code not in docs:
    ret2
  Mismatches in argument names:
    Position: 5 Code: ret2 Docs: ...

* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [77s/78s] OK
Examples with CPU or elapsed time > 5s
          user system elapsed
sextest 17.624  0.288  17.985
seabi   16.227  0.048  16.298
metrics 10.530  0.298  10.838
* 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

WARNING: There were 3 warnings.
NOTE: There were 4 notes.
See
  ‘/Users/biocbuild/bbs-3.0-bioc/meat/wateRmelon.Rcheck/00check.log’
for details.

wateRmelon.Rcheck/00install.out:

* installing *source* package ‘wateRmelon’ ...
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function from function ‘as.methylumi’ in package ‘wateRmelon’
in method for ‘betaqn’ with signature ‘bn="exprmethy450"’: no definition for class “exprmethy450”
in method for ‘fuks’ with signature ‘data="exprmethy450"’: no definition for class “exprmethy450”
in method for ‘genki’ with signature ‘bn="exprmethy450"’: no definition for class “exprmethy450”
in method for ‘dmrse’ with signature ‘betas="exprmethy450"’: no definition for class “exprmethy450”
in method for ‘dmrse_row’ with signature ‘betas="exprmethy450"’: no definition for class “exprmethy450”
in method for ‘dmrse_col’ with signature ‘betas="exprmethy450"’: no definition for class “exprmethy450”
in method for ‘seabi’ with signature ‘bn="exprmethy450"’: no definition for class “exprmethy450”
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (wateRmelon)

wateRmelon.Rcheck/wateRmelon-Ex.timings:

nameusersystemelapsed
BMIQ2.4610.0482.571
combo1.0840.0131.099
dasen2.5270.2292.758
dmrse2.6590.2322.892
genki2.5550.2352.791
iDMR0.0020.0010.003
melon0.1790.0140.194
metrics10.530 0.29810.838
pfilter0.3380.0150.353
seabi16.227 0.04816.298
sextest17.624 0.28817.985