BioC experimental data: CHECK report for dyebiasexamples on perceval

Package: dyebiasexamples

Version: 1.0.12

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch dyebiasexamples_1.0.12.tar.gz

StartedAt: 2014-04-04 10:34:56 -0700 (Fri, 04 Apr 2014)

EndedAt: 2014-04-04 10:57:15 -0700 (Fri, 04 Apr 2014)

EllapsedTime: 1339.2 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: dyebiasexamples.Rcheck

Warnings: 4

* using log directory ‘/Users/biocbuild/bbs-2.13-data-experiment/meat/dyebiasexamples.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘dyebiasexamples/DESCRIPTION’ ... OK
* this is package ‘dyebiasexamples’ version ‘1.0.12’
* checking package namespace information ... OK
* checking package dependencies ... OK
* 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 ‘dyebiasexamples’ can be installed ... [6s/8s] OK
* checking installed package size ... NOTE
  installed size is 40.2Mb
  sub-directories of 1Mb or more:
    data        5.3Mb
    extradata  34.8Mb
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... NOTE
File
  LICENSE
is not mentioned in the DESCRIPTION file.
* 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
Packages in Depends field not imported from:
  ‘GEOquery’ ‘marray’
  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 ... OK
* checking Rd files ... WARNING
checkRd: (3) dyebias.geo2marray.Rd:10-17: \synopsis will be removed in R 3.1.0
checkRd: (3) dyebias.umcu.proper.estimators.Rd:11-13: \synopsis will be removed in R 3.1.0
* 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 'dyebias.geo2marray':
dyebias.geo2marray
  Code: function(gse, slide.ids = NULL, type = "norm", gene.selector =
                 function(table) { T}, reporterid.name, cy3.name,
                 cy5.name, R.name = NULL, G.name = NULL, M.name = NULL,
                 A.name = NULL, Rf.name = NULL, Gf.name = NULL, Rb.name
                 = NULL, Gb.name = NULL)
  Docs: function(gse, slide.ids = NULL, type = "norm", gene.selector =
                 function(table) { TRUE}, reporterid.name, cy3.name,
                 cy5.name, R.name = NULL, G.name = NULL, M.name = NULL,
                 A.name = NULL, Rf.name = NULL, Gf.name = NULL, Rb.name
                 = NULL, Gb.name = NULL)
  Mismatches in argument default values:
    Name: 'gene.selector'
    Code: function(table) {
          T
      }
    Docs: function(table) {
          TRUE
      }

* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... WARNING
Files not of a type allowed in a ‘data’ directory:
  ‘README’
Please use e.g. ‘inst/extdata’ for non-R data files
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... WARNING
  
  Note: significantly better compression could be obtained
        by using R CMD build --resave-data
                old_size new_size compress
  data.norm.rda    2.1Mb    1.5Mb       xz
  data.raw.rda     3.2Mb    2.2Mb       xz
* checking files in ‘vignettes’ ... OK
* checking examples ... [9s/10s] OK
* checking PDF version of manual ... OK

WARNING: There were 4 warnings.
NOTE: There were 3 notes.
See
  ‘/Users/biocbuild/bbs-2.13-data-experiment/meat/dyebiasexamples.Rcheck/00check.log’
for details.

* installing *source* package ‘dyebiasexamples’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (dyebiasexamples)

name	user	system	elapsed
data.raw	1.397	0.029	1.439
dyebias.geo2marray	0.115	0.005	0.119
dyebias.umcu.proper.estimators	4.584	0.090	4.723