Package: AffyExpress

Version: 1.26.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch AffyExpress_1.26.0.tar.gz

StartedAt: 2013-05-01 01:55:22 -0700 (Wed, 01 May 2013)

EndedAt: 2013-05-01 01:57:44 -0700 (Wed, 01 May 2013)

EllapsedTime: 141.8 seconds

RetCode: 0

Status:  OK

CheckDir: AffyExpress.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/AffyExpress.Rcheck'
* using R version 3.0.0 Patched (2013-04-08 r62531)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'AffyExpress/DESCRIPTION' ... OK
* this is package 'AffyExpress' version '1.26.0'
* 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 'AffyExpress' can be installed ... [6s/7s] 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 ... OK
* checking R code for possible problems ... NOTE
AffyQA: warning in png(file = figure1): partial argument match of
  'file' to 'filename'
AffyQA: warning in png(file = figure1, height = 960): partial argument
  match of 'file' to 'filename'
AffyQA: warning in matrix(c(1, 3, 5, 7, 2, 4, 6, 7), nr = 4, ncol = 2):
  partial argument match of 'nr' to 'nrow'
AffyQA: warning in png(file = figure2): partial argument match of
  'file' to 'filename'
AffyQA: warning in plotAffyRNAdeg(deg, col = dum[1:size]): partial
  argument match of 'col' to 'cols'
AffyQA: warning in png(file = figure3): partial argument match of
  'file' to 'filename'
AffyQA: warning in png(file = figure4): partial argument match of
  'file' to 'filename'
AffyQA: warning in png(file = figure5): partial argument match of
  'file' to 'filename'
* 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 ... [63s/64s] OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
AffyInteraction         11.727  0.244  12.175
Filter                   6.623  0.120   6.923
interaction.result2html  5.971  0.089   6.244
AffyRegress              5.730  0.070   5.879
result2html              5.647  0.066   5.770
post.interaction         5.635  0.064   5.908
regress                  5.610  0.055   5.736
select.sig.gene          5.552  0.060   5.728
pre.process              5.506  0.059   5.685
* 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 was 1 note.
See
  '/Users/biocbuild/bbs-2.12-bioc/meat/AffyExpress.Rcheck/00check.log'
for details.

* installing *source* package 'AffyExpress' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (AffyExpress)

name	user	system	elapsed
AffyInteraction	11.727	0.244	12.175
AffyQA	0.012	0.004	0.018
AffyRegress	5.730	0.070	5.879
Filter	6.623	0.120	6.923
import.data	0.045	0.005	0.051
interaction.result2html	5.971	0.089	6.244
make.contrast	0.066	0.002	0.070
make.design	0.022	0.009	0.030
post.interaction	5.635	0.064	5.908
pre.process	5.506	0.059	5.685
regress	5.610	0.055	5.736
result2html	5.647	0.066	5.770
select.sig.gene	5.552	0.060	5.728