Package: charm

Version: 1.3.3

Command: /Library/Frameworks/R.framework/Versions/2.13/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch charm_1.3.3.tar.gz

StartedAt: 2011-03-17 15:55:11 -0700 (Thu, 17 Mar 2011)

EndedAt: 2011-03-17 16:00:09 -0700 (Thu, 17 Mar 2011)

EllapsedTime: 298.0 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: charm.Rcheck

Warnings: 2

* using log directory '/Users/biocbuild/bbs-2.8-bioc/meat/charm.Rcheck'
* using R version 2.13.0 Under development (unstable) (2011-03-06 r54683)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'charm/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'charm' version '1.3.3'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'charm' can be installed ... WARNING
Found the following significant warnings:
  Warning: 'DESCRIPTION' file has 'Encoding' field and re-encoding is not possible
  Warning: 'DESCRIPTION' file has 'Encoding' field and re-encoding is not possible
See '/Users/biocbuild/bbs-2.8-bioc/meat/charm.Rcheck/00install.out' for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level 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 name space can be loaded with stated dependencies ... OK
* checking whether the name space 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
dmrPlot_paired: no visible binding for global variable 'cgi'
dmrPlot_paired: no visible binding for global variable 'Mmusculus'
dmrPlot_paired: no visible binding for global variable 'Rnorvegicus'
dmrPlot_unpaired: no visible binding for global variable 'cgi'
dmrPlot_unpaired: no visible binding for global variable 'Mmusculus'
dmrPlot_unpaired: no visible binding for global variable 'Rnorvegicus'
regionPlot: no visible binding for global variable 'cgi'
regionPlot: no visible binding for global variable 'Mmusculus'
regionPlot: no visible binding for global variable 'Rnorvegicus'
* 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 'getControlIndex':
getControlIndex
  Code: function(dat, controlProbes = NULL, noCpGWindow = 1000,
                 subject, onlyGood = FALSE, matrix = TRUE)
  Docs: function(dat, controlProbes = c("CONTROL_PROBES",
                 "CONTROL_REGIONS"), noCpGWindow = 1000, subject,
                 onlyGood = FALSE, matrix = TRUE)
  Mismatches in argument default values:
    Name: 'controlProbes' Code: NULL Docs: c("CONTROL_PROBES", "CONTROL_REGIONS")

Codoc mismatches from documentation object 'normalizeBetweenSamples':
normalizeBetweenSamples
  Code: function(dat, copy = TRUE, m = "allQuantiles", untreated =
                 "none", enriched = "none", controlProbes = NULL,
                 controlIndex = NULL, excludeIndex = NULL, verbose =
                 FALSE)
  Docs: function(dat, copy = TRUE, m = "allQuantiles", untreated =
                 "none", enriched = "none", controlProbes =
                 c("CONTROL_PROBES", "CONTROL_REGIONS"), controlIndex =
                 NULL, excludeIndex = NULL, verbose = FALSE)
  Mismatches in argument default values:
    Name: 'controlProbes' Code: NULL Docs: c("CONTROL_PROBES", "CONTROL_REGIONS")

Codoc mismatches from documentation object 'normalizeWithinSamples':
normalizeWithinSamples
  Code: function(dat, copy = TRUE, method = "loess", scale = c(0.99,
                 0.99), controlProbes = NULL, controlIndex = NULL,
                 approx = TRUE, breaks = 1000, verbose = FALSE)
  Docs: function(dat, copy = TRUE, method = "loess", scale = c(0.99,
                 0.99), controlProbes = c("CONTROL_PROBES",
                 "CONTROL_REGIONS"), controlIndex = NULL, approx =
                 TRUE, breaks = 1000, verbose = FALSE)
  Mismatches in argument default values:
    Name: 'controlProbes' Code: NULL Docs: c("CONTROL_PROBES", "CONTROL_REGIONS")

* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... SKIPPED
* checking PDF version of manual ... OK

WARNING: There were 2 warnings, see
  '/Users/biocbuild/bbs-2.8-bioc/meat/charm.Rcheck/00check.log'
for details

* installing *source* package 'charm' ...
** R
** inst
** preparing package for lazy loading

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'browseVignettes()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation("pkgname")'.

Loading required package: mclust

by using mclust, invoked on its own or through another package,
you accept the license agreement in the mclust LICENSE file
and at http://www.stat.washington.edu/mclust/license.txt

Loading required package: nor1mix
Loading required package: spam
Package 'spam' is loaded. Spam version 0.23-0 (2010-09-01).
Type demo( spam) for some demos, help( Spam) for an overview
of this package.
Help for individual functions is optained by adding the
suffix '.spam' to the function name, e.g. 'help(chol.spam)'.

Attaching package: 'spam'

The following object(s) are masked from 'package:base':

    backsolve, forwardsolve, norm

 Use help(fields) for an overview of this library

library( fields, keep.source=TRUE) retains comments in the source code. 
Warning: 'DESCRIPTION' file has 'Encoding' field and re-encoding is not possible
Loading package bit1.1-6

package:bit (c) 2008/2009 Jens Oehlschlaegel (GPL-2)

creators: bit bitwhich

coercion: as.logical as.integer as.bit as.bitwhich which

operator: ! & | xor != == 

querying: print length any all min max range sum summary

bit access: length<- [ [<- [[ [[<-

for more help type ?bit

Warning: 'DESCRIPTION' file has 'Encoding' field and re-encoding is not possible
Loading package ff2.2-1

- getOption("fftempdir")=="/tmp/RtmpI9IEtA"

- getOption("ffextension")=="ff"

- getOption("ffdrop")==TRUE

- getOption("fffinonexit")==TRUE

- getOption("ffpagesize")==65536

- getOption("ffcaching")=="mmnoflush"  -- consider "ffeachflush" if your system stalls on large writes

- getOption("ffbatchbytes")==16777216 -- consider a different value for tuning your system

- getOption("ffmaxbytes")==536870912 -- consider a different value for tuning your system

** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

by using mclust, invoked on its own or through another package,
you accept the license agreement in the mclust LICENSE file
and at http://www.stat.washington.edu/mclust/license.txt

Welcome to charm version 1.3.3
Warning messages:
1: 'DESCRIPTION' file has 'Encoding' field and re-encoding is not possible 
2: 'DESCRIPTION' file has 'Encoding' field and re-encoding is not possible 

* DONE (charm)

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