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BioC experimental data: CHECK report for affydata on morelia

This page was generated on 2015-11-25 16:26:09 -0800 (Wed, 25 Nov 2015).

Package 3/258HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
affydata 1.19.0
Harris Jaffee
Snapshot Date: 2015-11-25 07:17:28 -0800 (Wed, 25 Nov 2015)
URL: https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs/affydata
Last Changed Rev: 3462 / Revision: 3504
Last Changed Date: 2015-10-13 13:20:35 -0700 (Tue, 13 Oct 2015)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  WARNINGS UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  WARNINGS  OK 
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ WARNINGS ] OK 

Summary

Package: affydata
Version: 1.19.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings affydata_1.19.0.tar.gz
StartedAt: 2015-11-25 10:04:17 -0800 (Wed, 25 Nov 2015)
EndedAt: 2015-11-25 10:05:40 -0800 (Wed, 25 Nov 2015)
EllapsedTime: 82.6 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: affydata.Rcheck
Warnings: 2

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings affydata_1.19.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.3-data-experiment/meat/affydata.Rcheck’
* using R Under development (unstable) (2015-11-08 r69614)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘affydata/DESCRIPTION’ ... OK
* this is package ‘affydata’ version ‘1.19.0’
* 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 ... [2s/10s] 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.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
     Package    LibPath                                                        
[1,] "affydata" "/Users/biocbuild/bbs-3.3-data-experiment/meat/affydata.Rcheck"
     Item       Title                        
[1,] "Dilution" "AffyBatch instance Dilution"
* 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
* DONE

Status: 2 WARNINGs, 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.3-data-experiment/meat/affydata.Rcheck/00check.log’
for details.


affydata.Rcheck/00install.out:

* 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    LibPath                                                        
[1,] "affydata" "/Users/biocbuild/bbs-3.3-data-experiment/meat/affydata.Rcheck"
     Item       Title                        
[1,] "Dilution" "AffyBatch instance Dilution"
* DONE (affydata)