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Package 22/609HostnameOS / ArchBUILDCHECKBUILD BIN
affyPara 1.18.0
Markus Schmidberger
Snapshot Date: 2013-03-24 16:21:20 -0700 (Sun, 24 Mar 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_11/madman/Rpacks/affyPara
Last Changed Rev: 70050 / Revision: 74773
Last Changed Date: 2012-10-01 15:16:24 -0700 (Mon, 01 Oct 2012)
lamb1 Linux (openSUSE 12.1) / x86_64  OK [ WARNINGS ]
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  WARNINGS  OK 
perceval Mac OS X Leopard (10.5.8) / i386  OK  WARNINGS  OK 

Summary

Package: affyPara
Version: 1.18.0
Command: /home/biocbuild/bbs-2.11-bioc/R/bin/R CMD check --no-vignettes --timings affyPara_1.18.0.tar.gz
StartedAt: 2013-03-24 23:03:26 -0700 (Sun, 24 Mar 2013)
EndedAt: 2013-03-24 23:04:51 -0700 (Sun, 24 Mar 2013)
EllapsedTime: 84.7 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: affyPara.Rcheck
Warnings: 1

Command output

* using log directory ‘/loc/home/biocbuild/bbs-2.11-bioc/meat/affyPara.Rcheck’
* using R version 2.15.3 (2013-03-01)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘affyPara/DESCRIPTION’ ... OK
* this is package ‘affyPara’ version ‘1.18.0’
* 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 whether package ‘affyPara’ can be installed ... OK
* 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 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 ... WARNING
Foreign function call with ‘PACKAGE’ argument in a different package:
  .Call("ReadHeader", ..., PACKAGE = "affyio")
Undeclared package in foreign function calls:
   ‘affyio’
See the chapter ‘System and foreign language interfaces’ of the
‘Writing R Extensions’ manual.
* checking R code for possible problems ... NOTE
File ‘affyPara/R/zzz.R’:
  .onLoad calls:
    require(affy)
    require(snow)

Package startup functions should not change the search path.
See section ‘Good practice’ in ?.onAttach.

MAplotPara: warning in drawMAplot(object, badQCu, meanchip, type, log,
  subset, span, pch = pch, ref.title, show.statistics, family.loess,
  verbose, ...): partial argument match of 'pch' to 'pchs'
MAplotSer: warning in drawMAplot(object, badQCu, meanchip, type, log,
  subset, span, pch = pch, ref.title, show.statistics, family.loess,
  verbose, ...): partial argument match of 'pch' to 'pchs'
grad_loglikPara: warning in get("px", env = .GlobalEnv): partial
  argument match of 'env' to 'envir'
* 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 installed files from ‘inst/doc’ ... NOTE
The following directories should probably not be installed:
  ‘fig’

Consider the use of a .Rinstignore file: see ‘Writing R Extensions’,
or move the vignette sources from ‘inst/doc’ to ‘vignettes’.
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
mergeSplitObjects 6.088   0.12   6.227
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignettes ... SKIPPED
* checking PDF version of manual ... OK

WARNING: There was 1 warning.
NOTE: There were 2 notes.
See
  ‘/loc/home/biocbuild/bbs-2.11-bioc/meat/affyPara.Rcheck/00check.log’
for details.

affyPara.Rcheck/00install.out:

* installing *source* package ‘affyPara’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘affyPara.Rnw’ 
   ‘vsnStudy.Rnw’ 
** testing if installed package can be loaded

* DONE (affyPara)

affyPara.Rcheck/affyPara-Ex.timings:

nameusersystemelapsed
MAplotPara0.0000.0000.001
bgcPara000
boxplotPara000
computeExprSetPara000
distributeFiles000
mergeSplitObjects6.0880.1206.227
normalizeAffyBatchConstantPara0.0000.0000.001
normalizeAffyBatchInvariantsetPara000
normalizeAffyBatchLoessPara000
normalizeAffyBatchLoessParaIter000
normalizeAffyBatchQuantilesPara000
preproPara0.0000.0000.001
qa0.0040.0000.000
readAffybatchPara000
removeDistributedFiles000
rmaPara000
snowReplace000
split2.2760.0242.379
vsnPara000