BioC 2.12: CHECK report for altcdfenvs on petty

Package: altcdfenvs

Version: 2.22.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch altcdfenvs_2.22.0.tar.gz

StartedAt: 2013-10-08 21:32:16 -0700 (Tue, 08 Oct 2013)

EndedAt: 2013-10-08 21:36:47 -0700 (Tue, 08 Oct 2013)

EllapsedTime: 270.8 seconds

RetCode: 0

Status:  OK

CheckDir: altcdfenvs.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/altcdfenvs.Rcheck'
* using R version 3.0.1 (2013-05-16)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* 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 ... [19s/20s] 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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [67s/68s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
removeIndex      27.244  0.245  27.591
matchAffyProbes  17.728  0.795  18.641
CdfEnvAffy-class 11.554  0.111  11.788
* 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	0.236	0.002	0.238
CdfEnvAffy-class	11.554	0.111	11.788
appendCdfEnvAffy	0.034	0.004	0.038
cdfenv	0.007	0.001	0.008
cdfenvEx	0.017	0.002	0.020
getxy.probeseq	0.013	0.001	0.013
index2xy	0.006	0.000	0.007
matchAffyProbes	17.728	0.795	18.641
plot.CdfEnvAffy	0.079	0.033	0.113
removeIndex	27.244	0.245	27.591
unique.CdfEnvAffy	0.002	0.004	0.006
utils.FASTA	0.016	0.010	0.027
validAffyBatch	0.003	0.004	0.006