BioC 2.12: CHECK report for affypdnn on george2

Package: affypdnn

Version: 1.34.0

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings affypdnn_1.34.0.tar.gz

StartedAt: 2013-10-08 23:58:02 -0700 (Tue, 08 Oct 2013)

EndedAt: 2013-10-09 00:04:11 -0700 (Wed, 09 Oct 2013)

EllapsedTime: 369.5 seconds

RetCode: 0

Status:  OK

CheckDir: affypdnn.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/affypdnn.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 ‘affypdnn/DESCRIPTION’ ... OK
* this is package ‘affypdnn’ version ‘1.34.0’
* 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 ‘affypdnn’ can be installed ... [5s/5s] OK
* checking installed package size ... NOTE
  installed size is 12.1Mb
  sub-directories of 1Mb or more:
    data  11.7Mb
* 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 ... 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'
* 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 installed files from ‘inst/doc’ ... OK
* checking examples ... [284s/293s] OK
Examples with CPU or elapsed time > 5s
                               user system elapsed
expressopdnn                140.508  2.232 145.982
generateExprVal.method.pdnn 109.147  0.188 113.055
find.params.pdnn             27.618  0.488  29.643
* 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/affypdnn.Rcheck/00check.log’
for details.

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

name	user	system	elapsed
chiptype.pdnn.params	0.012	0.000	0.011
expressopdnn	140.508	2.232	145.982
find.params.pdnn	27.618	0.488	29.643
generateExprVal.method.pdnn	109.147	0.188	113.055
matplotProbesPDNN	0.008	0.000	0.006
params.dilution	0.564	0.008	0.573
pdnn.params.chiptype	0.008	0.000	0.009
transform.ProbeSet	0.796	0.028	0.825