Package: altcdfenvs

Version: 2.12.0

Command: E:\biocbld\bbs-2.7-bioc\R\bin\R.exe CMD check --no-vignettes --timings altcdfenvs_2.12.0.tar.gz

StartedAt: 2011-04-07 05:43:42 -0700 (Thu, 07 Apr 2011)

EndedAt: 2011-04-07 05:46:26 -0700 (Thu, 07 Apr 2011)

EllapsedTime: 164.2 seconds

RetCode: 0

Status:  OK

CheckDir: altcdfenvs.Rcheck

Warnings: 0

* using log directory 'E:/biocbld/bbs-2.7-bioc/meat/altcdfenvs.Rcheck'
* using R version 2.12.2 (2011-02-25)
* using platform: i386-pc-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'altcdfenvs/DESCRIPTION' ... OK
* this is package 'altcdfenvs' version '2.12.0'
* 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 package directory ... OK
* checking for portable file names ... 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 data for non-ASCII characters ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... 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
  'openVignette()'. 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, mapply, order, paste, pmax, pmax.int, pmin,
    pmin.int, rbind, rep.int, table

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 new generic function for "plot" in "altcdfenvs"
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (altcdfenvs)

name	user	system	elapsed
AffyProbesMatch-class	0	0	0
CdfEnvAffy-class	7.08	0.02	7.09
appendCdfEnvAffy	0	0	0
cdfenv	0	0	0
cdfenvEx	0.00	0.02	0.01
getxy.probeseq	0	0	0
index2xy	0	0	0
matchAffyProbes	14.50	0.37	14.96
plot.CdfEnvAffy	0	0	0
removeIndex	22.07	0.03	22.52
unique.CdfEnvAffy	0	0	0
utils.FASTA	0.00	0.02	0.41
validAffyBatch	0	0	0