BioC experimental data: CHECK report for affydata on perceval

Package: affydata

Version: 1.11.20

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch affydata_1.11.20.tar.gz

StartedAt: 2014-04-04 10:13:16 -0700 (Fri, 04 Apr 2014)

EndedAt: 2014-04-04 10:15:32 -0700 (Fri, 04 Apr 2014)

EllapsedTime: 136.6 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: affydata.Rcheck

Warnings: 2

* using log directory ‘/Users/biocbuild/bbs-2.13-data-experiment/meat/affydata.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 ‘affydata/DESCRIPTION’ ... OK
* this is package ‘affydata’ version ‘1.11.20’
* 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 ‘affydata’ can be installed ... [4s/6s] OK
* checking installed package size ... NOTE
  installed size is 23.5Mb
  sub-directories of 1Mb or more:
    celfiles       16.2Mb
    data            4.4Mb
    extracelfiles   2.7Mb
* checking package directory ... OK
* checking ‘build’ 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 ... WARNING
Error: .onLoad failed in loadNamespace() for ‘affydata’, details:
  call: show(data(package = pkgname)$results)
  error: error in evaluating the argument ‘object’ in selecting a method for function ‘show’: Error: could not find function "data"
Execution halted

A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file.
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
Package in Depends field not imported from: ‘affy’
  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 ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* 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 ... WARNING
  
  Note: significantly better compression could be obtained
        by using R CMD build --resave-data
               old_size new_size compress
  Dilution.rda    4.4Mb    2.4Mb       xz
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... NONE
* checking for unstated dependencies in vignettes ... NOTE
‘::’ or ‘:::’ import not declared from: ‘Biobase’
* 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 2 warnings.
NOTE: There were 3 notes.
See
  ‘/Users/biocbuild/bbs-2.13-data-experiment/meat/affydata.Rcheck/00check.log’
for details.

* installing *source* package ‘affydata’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
     Package   
[1,] "affydata"
     LibPath                                                         
[1,] "/Users/biocbuild/bbs-2.13-data-experiment/meat/affydata.Rcheck"
     Item       Title                        
[1,] "Dilution" "AffyBatch instance Dilution"
* DONE (affydata)