Package: altcdfenvs

Version: 2.16.0

Command: D:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD check --no-vignettes --timings --no-multiarch altcdfenvs_2.16.0.tar.gz

StartedAt: 2012-01-09 01:05:01 -0800 (Mon, 09 Jan 2012)

EndedAt: 2012-01-09 01:07:47 -0800 (Mon, 09 Jan 2012)

EllapsedTime: 165.2 seconds

RetCode: 0

Status:  OK

CheckDir: altcdfenvs.Rcheck

Warnings: 0

* using log directory 'D:/biocbld/bbs-2.9-bioc/meat/altcdfenvs.Rcheck'
* using R version 2.14.1 (2011-12-22)
* using platform: x86_64-pc-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'altcdfenvs/DESCRIPTION' ... OK
* this is package 'altcdfenvs' version '2.16.0'
* 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 'altcdfenvs' can be installed ... OK
* checking installed package size ... 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 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 'altcdfenvs/R/zzz.R':
  .First.lib has wrong argument list 'libname, pkgname, where'
  .First.lib calls:
    library(affy, pos = 3)

Package startup functions should have two arguments with names starting
  with 'lib' and 'pkg', respectively.
Package startup functions should not change the search path.
See section 'Good practice' in ?.onAttach.

* 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 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
Warning in .simpleDuplicateClass(def, prev) :
  A specification for S3 class "connection" in package 'graph' seems equivalent to one from package 'IRanges' and is not turning on duplicate class definitions for this class
Warning in .simpleDuplicateClass(def, prev) :
  A specification for S3 class "file" in package 'graph' seems equivalent to one from package 'IRanges' and is not turning on duplicate class definitions for this class
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	0	0
CdfEnvAffy-class	7.33	0.06	7.39
appendCdfEnvAffy	0.02	0.00	0.02
cdfenv	0	0	0
cdfenvEx	0	0	0
getxy.probeseq	0	0	0
index2xy	0	0	0
matchAffyProbes	15.06	0.33	15.41
plot.CdfEnvAffy	0	0	0
removeIndex	17.55	0.05	17.59
unique.CdfEnvAffy	0	0	0
utils.FASTA	0.02	0.00	0.02
validAffyBatch	0	0	0