BioC 2.12: CHECK report for graphite on petty

Package: graphite

Version: 1.6.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch graphite_1.6.0.tar.gz

StartedAt: 2013-10-08 22:40:02 -0700 (Tue, 08 Oct 2013)

EndedAt: 2013-10-08 22:45:53 -0700 (Tue, 08 Oct 2013)

EllapsedTime: 351.7 seconds

RetCode: 0

Status:  OK

CheckDir: graphite.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/graphite.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 'graphite/DESCRIPTION' ... OK
* this is package 'graphite' version '1.6.0'
* 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 'graphite' can be installed ... [35s/35s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... NOTE
File
  LICENSE
is not mentioned in the DESCRIPTION file.
* 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 ... NOTE
  Note: found 16 marked UTF-8 strings
* 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 ... [123s/125s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
runClipperMulti 53.986  0.808  55.289
runClipper      31.098  0.925  32.183
runSPIA         13.200  0.484  13.878
* 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

NOTE: There were 2 notes.
See
  '/Users/biocbuild/bbs-2.12-bioc/meat/graphite.Rcheck/00check.log'
for details.

* installing *source* package 'graphite' ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (graphite)

name	user	system	elapsed
convertIdentifiers	3.482	0.280	3.767
cytoscapePlot	0.250	0.115	0.366
pathwayGraph	0.046	0.005	0.050
runClipper	31.098	0.925	32.183
runClipperMulti	53.986	0.808	55.289
runDEGraph	4.495	0.211	4.812
runDEGraphMulti	1.716	0.060	1.829
runSPIA	13.200	0.484	13.878
runTopologyGSA	2.627	0.066	2.743
runTopologyGSAMulti	1.413	0.030	1.452