BioC 2.13: CHECK report for altcdfenvs on perceval

Package: altcdfenvs

Version: 2.24.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch altcdfenvs_2.24.0.tar.gz

StartedAt: 2014-04-04 23:19:48 -0700 (Fri, 04 Apr 2014)

EndedAt: 2014-04-04 23:24:01 -0700 (Fri, 04 Apr 2014)

EllapsedTime: 252.6 seconds

RetCode: 0

Status:  OK

CheckDir: altcdfenvs.Rcheck

Warnings: 0

* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/altcdfenvs.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘altcdfenvs/DESCRIPTION’ ... OK
* this is package ‘altcdfenvs’ version ‘2.24.0’
* 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 ... [16s/17s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ 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 dependencies in R code ... NOTE
Packages in Depends field not imported from:
  ‘Biobase’ ‘Biostrings’ ‘hypergraph’ ‘makecdfenv’ ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* 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 for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘altcdfenvs.Rnw’, ‘modify.Rnw’, ‘ngenomeschips.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [63s/64s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
matchAffyProbes  21.711  0.995  23.126
removeIndex      21.866  0.300  22.932
CdfEnvAffy-class  8.507  0.168   9.152
* 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There were 2 notes.
See
  ‘/Users/biocbuild/bbs-2.13-bioc/meat/altcdfenvs.Rcheck/00check.log’
for details.

* 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	0.009	0.001	0.011
CdfEnvAffy-class	8.507	0.168	9.152
appendCdfEnvAffy	0.05	0.01	0.06
cdfenv	0.008	0.002	0.010
cdfenvEx	0.018	0.003	0.021
getxy.probeseq	0.008	0.001	0.009
index2xy	0.009	0.001	0.010
matchAffyProbes	21.711	0.995	23.126
plot.CdfEnvAffy	0.001	0.004	0.005
removeIndex	21.866	0.300	22.932
unique.CdfEnvAffy	0.002	0.004	0.006
utils.FASTA	0.012	0.011	0.023
validAffyBatch	0.001	0.004	0.007