BioC 3.4: CHECK report for graphite on morelia

Package: graphite

Version: 1.20.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings graphite_1.20.1.tar.gz

StartedAt: 2017-04-15 03:14:32 -0700 (Sat, 15 Apr 2017)

EndedAt: 2017-04-15 03:21:06 -0700 (Sat, 15 Apr 2017)

EllapsedTime: 393.7 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 graphite_1.20.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/graphite.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘graphite/DESCRIPTION’ ... OK
* this is package ‘graphite’ version ‘1.20.1’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Packages which this enhances but not available for checking:
  ‘DEGraph’ ‘RCytoscape’ ‘RCy3’
* 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 ... 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 ... NOTE
Package unavailable to check Rd xrefs: ‘DEGraph’
* 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 ... OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
runClipperMulti 123.193  1.648 125.063
runClipper       19.887  0.454  27.680
runSPIA           5.347  0.545  77.059
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* 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
* DONE

Status: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.4-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
as.list.DeprecatedPathwayList	1.958	0.338	3.076
as.list.PathwayList	0.161	0.031	0.288
buildPathway	0.008	0.001	0.015
convertIdentifiers	0.888	0.020	1.372
cytoscapePlot	0.001	0.000	0.001
pathwayDatabases	0.020	0.001	0.031
pathwayGraph	0.047	0.000	0.049
pathways	0.001	0.000	0.001
runClipper	19.887	0.454	27.680
runClipperMulti	123.193	1.648	125.063
runDEGraph	0.002	0.000	0.007
runDEGraphMulti	0.002	0.000	0.002
runSPIA	5.347	0.545	77.059
runTopologyGSA	1.028	0.024	1.932
runTopologyGSAMulti	0.717	0.021	0.739