BioC 2.12: CHECK report for altcdfenvs on george2

Package: altcdfenvs

Version: 2.22.0

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings altcdfenvs_2.22.0.tar.gz

StartedAt: 2013-10-09 00:03:38 -0700 (Wed, 09 Oct 2013)

EndedAt: 2013-10-09 00:08:37 -0700 (Wed, 09 Oct 2013)

EllapsedTime: 298.4 seconds

RetCode: 0

Status:  OK

CheckDir: altcdfenvs.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/altcdfenvs.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 ‘altcdfenvs/DESCRIPTION’ ... OK
* this is package ‘altcdfenvs’ version ‘2.22.0’
* 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 ‘altcdfenvs’ can be installed ... [20s/21s] 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 ... 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 installed files from ‘inst/doc’ ... OK
* checking examples ... [76s/79s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
matchAffyProbes  28.210  0.504  29.720
removeIndex      25.873  0.052  26.777
CdfEnvAffy-class 10.585  0.100  11.389
* 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
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”
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (altcdfenvs)

name	user	system	elapsed
AffyProbesMatch-class	0.384	0.008	0.411
CdfEnvAffy-class	10.585	0.100	11.389
appendCdfEnvAffy	0.048	0.000	0.050
cdfenv	0.012	0.000	0.012
cdfenvEx	0.016	0.000	0.018
getxy.probeseq	0.016	0.000	0.014
index2xy	0.012	0.000	0.014
matchAffyProbes	28.210	0.504	29.720
plot.CdfEnvAffy	0.008	0.000	0.005
removeIndex	25.873	0.052	26.777
unique.CdfEnvAffy	0.004	0.000	0.004
utils.FASTA	0.012	0.004	0.018
validAffyBatch	0.004	0.000	0.004