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Package 23/609HostnameOS / ArchBUILDCHECKBUILD BIN
affypdnn 1.32.0
Laurent Gautier
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/affypdnn
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  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
perceval Mac OS X Leopard (10.5.8) / i386  OK [ OK ] OK 

Summary

Package: affypdnn
Version: 1.32.0
Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch affypdnn_1.32.0.tar.gz
StartedAt: 2013-03-24 22:26:05 -0700 (Sun, 24 Mar 2013)
EndedAt: 2013-03-24 22:29:52 -0700 (Sun, 24 Mar 2013)
EllapsedTime: 227.1 seconds
RetCode: 0
Status:  OK 
CheckDir: affypdnn.Rcheck
Warnings: 0

Command output

* using log directory '/Users/biocbuild/bbs-2.11-bioc/meat/affypdnn.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 'affypdnn/DESCRIPTION' ... OK
* this is package 'affypdnn' version '1.32.0'
* 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 'affypdnn' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 12.0Mb
  sub-directories of 1Mb or more:
    data  11.7Mb
* 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 ... OK
* checking R code for possible problems ... NOTE
File 'affypdnn/R/zzz.R':
  .onLoad calls:
    require(affy)
    cat("registering new summary method 'pdnn'.\n")
    cat("registering new pmcorrect method 'pdnn' and 'pdnnpredict'.\n")

Package startup functions should not change the search path.
Package startup functions should use 'packageStartupMessage' to
  generate messages.
See section 'Good practice' in ?.onAttach.

pmcorrect.pdnn: warning in matrix(as.logical(NA), nr = nrow(probes), nc
  = ncol(probes)): partial argument match of 'nr' to 'nrow'
pmcorrect.pdnn: warning in matrix(as.logical(NA), nr = nrow(probes), nc
  = ncol(probes)): partial argument match of 'nc' to 'ncol'
Found .Internal call in the following function:
  'pdnn.params.chiptype'
with calls to .Internal functions
  'substr'

Packages should not call .Internal(): it is not part of the API, for
use only by R itself and subject to change without notice.
* 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 ... OK
* checking sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                              user system elapsed
expressopdnn                64.746 14.974  82.703
generateExprVal.method.pdnn 48.385 13.910  63.594
find.params.pdnn            17.100  3.427  21.579
* 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
  '/Users/biocbuild/bbs-2.11-bioc/meat/affypdnn.Rcheck/00check.log'
for details.

affypdnn.Rcheck/00install.out:

* installing *source* package 'affypdnn' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   'affypdnn.Rnw' 
** testing if installed package can be loaded
registering new summary method 'pdnn'.
registering new pmcorrect method 'pdnn' and 'pdnnpredict'.

* DONE (affypdnn)

affypdnn.Rcheck/affypdnn-Ex.timings:

nameusersystemelapsed
chiptype.pdnn.params0.0020.0020.005
expressopdnn64.74614.97482.703
find.params.pdnn17.100 3.42721.579
generateExprVal.method.pdnn48.38513.91063.594
matplotProbesPDNN000
params.dilution0.6690.0260.714
pdnn.params.chiptype0.0000.0010.000
transform.ProbeSet0.6170.0670.700