BioC experimental data: CHECK report for dyebiasexamples on george2

Package: dyebiasexamples

Version: 1.0.10

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings dyebiasexamples_1.0.10.tar.gz

StartedAt: 2013-10-08 12:39:01 -0700 (Tue, 08 Oct 2013)

EndedAt: 2013-10-08 12:42:14 -0700 (Tue, 08 Oct 2013)

EllapsedTime: 193.1 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: dyebiasexamples.Rcheck

Warnings: 4

* using log directory ‘/home/biocbuild/bbs-2.12-data-experiment/meat/dyebiasexamples.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 ‘dyebiasexamples/DESCRIPTION’ ... OK
* this is package ‘dyebiasexamples’ version ‘1.0.10’
* 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 ... [7s/8s] OK
* checking installed package size ... NOTE
  installed size is 40.3Mb
  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 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 ... 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 installed files from ‘inst/doc’ ... OK
* checking examples ... [10s/11s] OK
* checking PDF version of manual ... OK

WARNING: There were 4 warnings.
NOTE: There were 2 notes.
See
  ‘/home/biocbuild/bbs-2.12-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	1.716	0.040	2.787
dyebias.geo2marray	0.004	0.004	0.016
dyebias.umcu.proper.estimators	4.608	0.060	4.807