BioC 2.12: CHECK report for wateRmelon on george2

Package: wateRmelon

Version: 1.0.3

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings wateRmelon_1.0.3.tar.gz

StartedAt: 2013-10-09 05:25:13 -0700 (Wed, 09 Oct 2013)

EndedAt: 2013-10-09 05:37:03 -0700 (Wed, 09 Oct 2013)

EllapsedTime: 710.3 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: wateRmelon.Rcheck

Warnings: 3

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/wateRmelon.Rcheck’
* using R version 3.0.1 (2013-05-16)
* using platform: x86_64-unknown-linux-gnu (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 ‘1.0.3’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: ‘IMA’
* 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 ... [66s/68s] WARNING
Found the following significant warnings:
  Warning: 'IlluminaHumanMethylation450k.db' is deprecated.
  Warning: 'IlluminaHumanMethylation450k.db' is deprecated.
See ‘/home/biocbuild/bbs-2.12-bioc/meat/wateRmelon.Rcheck/00install.out’ for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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 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
beadcount: no visible global function definition for ‘getProbeInfo’
beadcount: no visible global function definition for ‘getManifestInfo’
got: no visible global function definition for ‘getProbeInfo’
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 binding for global
  variable ‘probeAnnotationsCategory’
preprocessIlluminaMethylation: no visible binding for global variable
  ‘projectName’
betaqn,MethylSet: no visible global function definition for ‘getBeta’
betaqn,RGChannelSet: no visible global function definition for
  ‘getBeta’
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’
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,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,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 ... OK
* checking for code/documentation mismatches ... WARNING
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 installed files from ‘inst/doc’ ... OK
* checking examples ... [142s/143s] WARNING
Found the following significant warnings:

  Warning: ‘IlluminaHumanMethylation450k.db’ is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Examples with CPU or elapsed time > 5s
          user system elapsed
sextest 24.445  0.024  24.470
metrics 21.897  0.140  22.143
seabi   20.150  0.016  20.188
dasen   11.945  0.088  12.225
dmrse   10.936  0.056  11.144
genki   10.661  0.016  10.901
BMIQ     5.577  0.036   6.206
* 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 3 warnings.
NOTE: There were 2 notes.
See
  ‘/home/biocbuild/bbs-2.12-bioc/meat/wateRmelon.Rcheck/00check.log’
for details.

* installing *source* package ‘wateRmelon’ ...
** R
** data
** inst
** preparing package for lazy loading
Warning: replacing previous import ‘image’ when loading ‘graphics’
Warning: replacing previous import ‘nleqslv’ when loading ‘nleqslv’
Warning: 'IlluminaHumanMethylation450k.db' is deprecated.
Use 'FDb.InfiniumMethylation.hg19' instead.
Use 'FDb.InfiniumMethylation.hg18' instead.
Use 'mapToGenome() function in minfi or methylumi' instead.
See help("Deprecated")
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
Warning: replacing previous import ‘image’ when loading ‘graphics’
Warning: replacing previous import ‘nleqslv’ when loading ‘nleqslv’
Warning: 'IlluminaHumanMethylation450k.db' is deprecated.
Use 'FDb.InfiniumMethylation.hg19' instead.
Use 'FDb.InfiniumMethylation.hg18' instead.
Use 'mapToGenome() function in minfi or methylumi' instead.
See help("Deprecated")
* DONE (wateRmelon)

name	user	system	elapsed
BMIQ	5.577	0.036	6.206
combo	3.504	0.048	3.550
dasen	11.945	0.088	12.225
dmrse	10.936	0.056	11.144
genki	10.661	0.016	10.901
iDMR	0.112	0.004	0.115
melon	0.328	0.012	0.340
metrics	21.897	0.140	22.143
pfilter	0.792	0.020	0.822
seabi	20.150	0.016	20.188
sextest	24.445	0.024	24.470