Package: altcdfenvs

Version: 2.15.0

Command: /Library/Frameworks/R.framework/Versions/2.14/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch altcdfenvs_2.15.0.tar.gz

StartedAt: 2011-06-22 01:14:08 -0700 (Wed, 22 Jun 2011)

EndedAt: 2011-06-22 01:17:46 -0700 (Wed, 22 Jun 2011)

EllapsedTime: 217.7 seconds

RetCode: 0

Status:  OK

CheckDir: altcdfenvs.Rcheck

Warnings: 0

* using log directory ‘/Users/biocbuild/bbs-2.9-bioc/meat/altcdfenvs.Rcheck’
* using R version 2.14.0 Under development (unstable) (2011-06-03 r56037)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘altcdfenvs/DESCRIPTION’ ... OK
* this is package ‘altcdfenvs’ version ‘2.15.0’
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package ‘altcdfenvs’ 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 ... 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 examples ... OK
* 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

* installing *source* package ‘altcdfenvs’ ...
** R
** data
** inst
** preparing package for lazy loading

Welcome to Bioconductor

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

Loading required package: IRanges

Attaching package: ‘IRanges’

The following object(s) are masked from ‘package:Biobase’:

    updateObject

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

    Map, cbind, eval, intersect, mapply, order, paste, pmax, pmax.int,
    pmin, pmin.int, rbind, rep.int, setdiff, table, union

Loading required package: graph

Attaching package: ‘graph’

The following object(s) are masked from ‘package:Biostrings’:

    complement


Attaching package: ‘hypergraph’

The following object(s) are masked from ‘package:IRanges’:

    head, tail

The following object(s) are masked from ‘package:utils’:

    head, tail

NOTE: arguments in definition for validity method for class 'AffyProbesMatch' changed from (obj) to (object)
in method for ‘toHypergraph’ with signature ‘"CdfEnvAffy"’: no definition for class "CdfEnvAffy"
Creating a generic function for "plot" from package "graphics" in package “altcdfenvs”
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   ‘altcdfenvs.Rnw’ 
   ‘modify.Rnw’ 
   ‘ngenomeschips.Rnw’ 
** testing if installed package can be loaded

* DONE (altcdfenvs)

name	user	system	elapsed
AffyProbesMatch-class	0.002	0.000	0.002
CdfEnvAffy-class	8.983	0.046	9.206
appendCdfEnvAffy	0.008	0.002	0.008
cdfenv	0.000	0.000	0.001
cdfenvEx	0.004	0.001	0.005
getxy.probeseq	0.000	0.001	0.000
index2xy	0	0	0
matchAffyProbes	14.514	1.236	16.009
plot.CdfEnvAffy	0.000	0.000	0.001
removeIndex	24.942	0.122	25.315
unique.CdfEnvAffy	0.000	0.000	0.001
utils.FASTA	0.011	0.002	0.012
validAffyBatch	0	0	0