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 |
* using log directory '/Users/biocbuild/bbs-2.11-bioc/meat/affyPara.Rcheck'
* using R version 2.15.3 (2013-03-01)
* 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 '1.18.0'
* 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 sizes of PDF files under 'inst/doc' ... NOTE
'qpdf' made some significant size reductions:
compacted 'vsnAddonBoxplots_20-40-60.pdf' from 515Kb to 45Kb
compacted 'vsnStudy.pdf' from 2095Kb to 318Kb
compacted 'vsnSubsamplesBoxplot_25.pdf' from 213Kb to 20Kb
compacted 'vsnSubsamplesBoxplot_50.pdf' from 529Kb to 44Kb
consider running tools::compactPDF() on these files
* 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 4.819 0.711 5.807
* 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 3 notes.
See
'/Users/biocbuild/bbs-2.11-bioc/meat/affyPara.Rcheck/00check.log'
for details.