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BioC 2.12: CHECK report for wateRmelon on petty

This page was generated on 2013-10-09 09:40:17 -0700 (Wed, 09 Oct 2013).

Package 660/671HostnameOS / ArchBUILDCHECKBUILD BIN
wateRmelon 1.0.3
Leo
Snapshot Date: 2013-10-08 17:00:48 -0700 (Tue, 08 Oct 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_12/madman/Rpacks/wateRmelon
Last Changed Rev: 77240 / Revision: 81334
Last Changed Date: 2013-06-06 03:19:35 -0700 (Thu, 06 Jun 2013)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK  WARNINGS 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  WARNINGS  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK [ WARNINGS ] OK 

Summary

Package: wateRmelon
Version: 1.0.3
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch wateRmelon_1.0.3.tar.gz
StartedAt: 2013-10-09 00:09:02 -0700 (Wed, 09 Oct 2013)
EndedAt: 2013-10-09 00:16:50 -0700 (Wed, 09 Oct 2013)
EllapsedTime: 468.7 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: wateRmelon.Rcheck
Warnings: 3

Command output

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/wateRmelon.Rcheck'
* using R version 3.0.1 (2013-05-16)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* 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 ... [56s/56s] WARNING
Found the following significant warnings:
  Warning: 'IlluminaHumanMethylation450k.db' is deprecated.
  Warning: 'IlluminaHumanMethylation450k.db' is deprecated.
See '/Users/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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [76s/76s] 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 15.522  0.513  16.036
seabi   11.549  0.025  11.575
metrics  9.860  0.505  10.374
dasen    4.690  0.494   5.184
* 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
  '/Users/biocbuild/bbs-2.12-bioc/meat/wateRmelon.Rcheck/00check.log'
for details.

wateRmelon.Rcheck/00install.out:

* 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)

wateRmelon.Rcheck/wateRmelon-Ex.timings:

nameusersystemelapsed
BMIQ2.9840.0713.055
combo1.7070.0441.750
dasen4.6900.4945.184
dmrse4.1730.5084.681
genki4.1990.4854.683
iDMR0.0040.0030.006
melon0.6580.0190.677
metrics 9.860 0.50510.374
pfilter0.4560.0280.484
seabi11.549 0.02511.575
sextest15.522 0.51316.036