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BioC 2.12: CHECK report for affyPara on george2

This page was generated on 2013-10-09 09:37:27 -0700 (Wed, 09 Oct 2013).

Package 22/671HostnameOS / ArchBUILDCHECKBUILD BIN
affyPara 1.20.0
Markus Schmidberger
Snapshot Date: 2013-10-08 17:00:48 -0700 (Tue, 08 Oct 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_12/madman/Rpacks/affyPara
Last Changed Rev: 75263 / Revision: 81334
Last Changed Date: 2013-04-03 14:32:27 -0700 (Wed, 03 Apr 2013)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK [ OK ]
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK 

Summary

Package: affyPara
Version: 1.20.0
Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings affyPara_1.20.0.tar.gz
StartedAt: 2013-10-08 23:57:37 -0700 (Tue, 08 Oct 2013)
EndedAt: 2013-10-08 23:59:47 -0700 (Tue, 08 Oct 2013)
EllapsedTime: 130.4 seconds
RetCode: 0
Status:  OK 
CheckDir: affyPara.Rcheck
Warnings: 0

Command output

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/affyPara.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 ‘affyPara/DESCRIPTION’ ... OK
* this is package ‘affyPara’ version ‘1.20.0’
* 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 ‘affyPara’ can be installed ... [9s/10s] OK
* checking installed package size ... OK
* checking package 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 ... 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 ... NOTE
Foreign function call with ‘PACKAGE’ argument in a different package:
  .Call("ReadHeader", ..., PACKAGE = "affyio")
See the chapter ‘System and foreign language interfaces’ of the
‘Writing R Extensions’ manual.
* 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 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 ... [19s/19s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
mergeSplitObjects 11.008  0.304  11.316
* 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

NOTE: There were 2 notes.
See
  ‘/home/biocbuild/bbs-2.12-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
** testing if installed package can be loaded
* DONE (affyPara)

affyPara.Rcheck/affyPara-Ex.timings:

nameusersystemelapsed
MAplotPara0.0200.0000.018
bgcPara0.0160.0040.022
boxplotPara0.0120.0120.025
computeExprSetPara0.0160.0120.027
distributeFiles0.0160.0040.017
mergeSplitObjects11.008 0.30411.316
normalizeAffyBatchConstantPara0.0040.0000.006
normalizeAffyBatchInvariantsetPara0.0120.0000.009
normalizeAffyBatchLoessPara0.0080.0000.009
normalizeAffyBatchLoessParaIter0.0440.0000.044
normalizeAffyBatchQuantilesPara0.0080.0000.010
preproPara0.0480.0000.049
qa0.0120.0000.012
readAffybatchPara0.0160.0000.013
removeDistributedFiles0.0120.0000.010
rmaPara0.0080.0000.010
snowReplace0.0040.0000.006
split3.1450.0643.210
vsnPara0.0080.0000.010