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Package 16/444HostnameOS / ArchBUILDCHECKBUILD BIN
affyPara 1.11.5
Markus Schmidberger
Snapshot Date: 2011-03-17 11:16:30 -0700 (Thu, 17 Mar 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/affyPara
Last Changed Rev: 53815 / Revision: 53825
Last Changed Date: 2011-03-17 01:16:12 -0700 (Thu, 17 Mar 2011)
lamb1 Linux (openSUSE 11.3) / x86_64  OK  WARNINGS 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK  WARNINGS  OK 
gewurz Windows Server 2008 R2 Enterprise (64-bit) / x64  OK  WARNINGS  OK 
pelham Mac OS X Leopard (10.5.8) / i386  OK  WARNINGS  OK 
petty Mac OS X Snow Leopard (10.6.6) / i386  OK [ WARNINGS ] OK 

Summary

Package: affyPara
Version: 1.11.5
Command: /Library/Frameworks/R.framework/Versions/2.13/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch affyPara_1.11.5.tar.gz
StartedAt: 2011-03-17 15:26:19 -0700 (Thu, 17 Mar 2011)
EndedAt: 2011-03-17 15:27:36 -0700 (Thu, 17 Mar 2011)
EllapsedTime: 76.6 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: affyPara.Rcheck
Warnings: 1

Command output

* using log directory '/Users/biocbuild/bbs-2.8-bioc/meat/affyPara.Rcheck'
* using R version 2.13.0 Under development (unstable) (2011-03-06 r54683)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'affyPara/DESCRIPTION' ... OK
* this is package 'affyPara' version '1.11.5'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... 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 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 name space can be loaded with stated dependencies ... OK
* checking whether the name space 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 ... OK
* 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 'preproPara':
preproPara
  Code: function(object, cluster, bgcorrect = TRUE, bgcorrect.method =
                 NULL, bgcorrect.param = list(), normalize = TRUE,
                 normalize.method = NULL, normalize.param = list(),
                 pmcorrect.method = NULL, pmcorrect.param = list(),
                 summary.method = NULL, summary.param = list(), ids =
                 NULL, phenoData = new("AnnotatedDataFrame"), cdfname =
                 NULL, verbose = getOption("verbose"), ...)
  Docs: function(object, cluster, bgcorrect = TRUE, bgcorrect.method =
                 NULL, bgcorrect.param = list(), normalize = TRUE,
                 normalize.method = NULL, normalize.param = list(),
                 pmcorrect.method = NULL, pmcorrect.param = list(),
                 summary.method = NULL, summary.param = list(), ids =
                 NULL, phenoData = new("AnnotatedDataFrame"), cdfname =
                 NULL, verbose = getOption("verbose"))
  Argument names in code not in docs:
    ...

Codoc mismatches from documentation object 'vsnPara':
justvsnPara
  Code: function(object, ..., cluster, verbose = getOption("verbose"))
  Docs: function(object, cluster, ..., verbose = getOption("verbose"))
  Mismatches in argument names:
    Position: 2 Code: ... Docs: cluster
    Position: 3 Code: cluster Docs: ...

* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... SKIPPED
* checking PDF version of manual ... OK

WARNING: There was 1 warning, see
  '/Users/biocbuild/bbs-2.8-bioc/meat/affyPara.Rcheck/00check.log'
for details

affyPara.Rcheck/00install.out:

* installing *source* package 'affyPara' ...
** R
** inst
** preparing package for lazy loading
Loading required package: Biobase

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'browseVignettes()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation("pkgname")'.


Attaching package: 'snow'

The following object(s) are masked from 'package:base':

    enquote

Loading required package: tcltk
Loading Tcl/Tk interface ... done
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (affyPara)

affyPara.Rcheck/affyPara-Ex.timings:

nameusersystemelapsed
MAplotPara0.0000.0000.001
bgcPara0.0000.0000.001
boxplotPara000
computeExprSetPara0.0000.0000.001
distributeFiles000
mergeSplitObjects3.2960.3103.606
normalizeAffyBatchConstantPara000
normalizeAffyBatchInvariantsetPara000
normalizeAffyBatchLoessPara0.0000.0010.001
normalizeAffyBatchLoessParaIter000
normalizeAffyBatchQuantilesPara000
preproPara0.0000.0000.001
qa000
readAffybatchPara0.0000.0010.000
removeDistributedFiles000
rmaPara0.0000.0000.001
snowReplace0.0000.0010.000
split1.3810.2091.590
vsnPara0.0000.0000.001