BioC 2.14: CHECK report for graphite on morelia

Package: graphite

Version: 1.10.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch graphite_1.10.1.tar.gz

StartedAt: 2014-10-07 23:20:56 -0700 (Tue, 07 Oct 2014)

EndedAt: 2014-10-07 23:25:55 -0700 (Tue, 07 Oct 2014)

EllapsedTime: 298.7 seconds

RetCode: 0

Status:  OK

CheckDir: graphite.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch graphite_1.10.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/graphite.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-apple-darwin13.1.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘graphite/DESCRIPTION’ ... OK
* this is package ‘graphite’ version ‘1.10.1’
* 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 ... [20s/21s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ 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 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 28 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 files in ‘vignettes’ ... OK
* checking examples ... [164s/167s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
runClipperMulti 126.589  1.535 128.437
runClipper       17.933  0.395  18.342
runSPIA           6.853  0.184   7.083
runDEGraph        1.846  0.086   5.051
* 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-2.14-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	1.239	0.094	1.337
cytoscapePlot	0.000	0.001	0.000
pathwayGraph	0.027	0.000	0.027
runClipper	17.933	0.395	18.342
runClipperMulti	126.589	1.535	128.437
runDEGraph	1.846	0.086	5.051
runDEGraphMulti	0.627	0.012	0.639
runSPIA	6.853	0.184	7.083
runTopologyGSA	1.615	0.018	1.648
runTopologyGSAMulti	0.591	0.004	0.596