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BioC 2.14: CHECK report for wateRmelon on zin2

This page was generated on 2014-10-08 08:49:47 -0700 (Wed, 08 Oct 2014).

Package 813/824HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
wateRmelon 1.4.0
Leo
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/wateRmelon
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: wateRmelon
Version: 1.4.0
Command: /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings wateRmelon_1.4.0.tar.gz
StartedAt: 2014-10-08 03:36:05 -0700 (Wed, 08 Oct 2014)
EndedAt: 2014-10-08 03:42:10 -0700 (Wed, 08 Oct 2014)
EllapsedTime: 364.9 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: wateRmelon.Rcheck
Warnings: 4

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings wateRmelon_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-2.14-bioc/meat/wateRmelon.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 ‘wateRmelon/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘wateRmelon’ version ‘1.4.0’
* 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’
  ‘IlluminaHumanMethylation450k.db’ ‘ROC’
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 ... [36s/36s] WARNING
Found the following significant warnings:
  Warning: 'IlluminaHumanMethylation450k.db' is deprecated.
See ‘/home/biocbuild/bbs-2.14-bioc/meat/wateRmelon.Rcheck/00install.out’ for details.
* 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 ... 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' call to ‘methylumi’ which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘IlluminaHumanMethylation450k.db’ ‘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.
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
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’
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’ ‘dfort’ ‘genall’ ‘genme’ ‘genus’ ‘goodSNP’
All user-level objects in a package should have documentation entries.
See the chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 files in ‘vignettes’ ... OK
* checking examples ... [65s/65s] 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 13.637  0.012  13.670
seabi   11.569  0.008  11.597
metrics  8.829  0.048   8.919
* 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 4 warnings.
NOTE: There were 4 notes.
See
  ‘/home/biocbuild/bbs-2.14-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 by ‘graphics::image’ when loading ‘methylumi’
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 by ‘graphics::image’ when loading ‘methylumi’
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
BMIQ2.6840.0122.702
combo1.0040.0081.013
dasen3.1600.0043.170
dmrse2.7320.0002.735
genki2.7720.0002.776
iDMR0.0000.0000.002
melon0.1680.0000.166
metrics8.8290.0488.919
pfilter0.3120.0080.321
seabi11.569 0.00811.597
sextest13.637 0.01213.670