BioC 2.13: CHECK report for PANR on perceval

Package: PANR

Version: 1.8.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch PANR_1.8.0.tar.gz

StartedAt: 2014-04-05 03:13:53 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 03:15:16 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 82.8 seconds

RetCode: 0

Status:  OK

CheckDir: PANR.Rcheck

Warnings: 0

* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/PANR.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 ‘PANR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘PANR’ version ‘1.8.0’
* 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 ‘PANR’ can be installed ... [3s/4s] 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 ... 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 for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘PANR-Vignette.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [31s/32s] OK
Examples with CPU or elapsed time > 5s
          user system elapsed
fitNULL 26.346  0.374  27.166
* 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 was 1 note.
See
  ‘/Users/biocbuild/bbs-2.13-bioc/meat/PANR.Rcheck/00check.log’
for details.

* installing *source* package ‘PANR’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (PANR)

name	user	system	elapsed
BetaMixture-class	0.006	0.001	0.007
PAN-class	0.006	0.001	0.007
SNR2p	0.006	0.000	0.005
assoScore	0.028	0.002	0.030
buildPAN	1.655	0.066	1.739
cosineSim	0.009	0.001	0.011
data-Bakal2007	0.027	0.008	0.034
exportPAN	0.006	0.002	0.008
fitBM	0.006	0.002	0.008
fitNULL	26.346	0.374	27.166
infer	0.899	0.048	0.992
p2SNR	0.015	0.011	0.026
permNULL	0.024	0.007	0.032
pvclustModule	0.007	0.003	0.011
sigModules	0.009	0.002	0.011
summarize	0.028	0.006	0.070
view	0.318	0.039	0.418
viewLegend	0.004	0.003	0.007
viewNestedModules	0.008	0.005	0.013
viewPAN	0.005	0.003	0.009