BioC 3.1: CHECK report for graphite on petty

Package: graphite

Version: 1.14.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings graphite_1.14.1.tar.gz

StartedAt: 2015-10-08 23:30:45 -0700 (Thu, 08 Oct 2015)

EndedAt: 2015-10-08 23:38:53 -0700 (Thu, 08 Oct 2015)

EllapsedTime: 488.1 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_1.14.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/graphite.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘graphite/DESCRIPTION’ ... OK
* this is package ‘graphite’ version ‘1.14.1’
* 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 ... [35s/36s] OK
* checking installed package size ... NOTE
  installed size is 11.7Mb
  sub-directories of 1Mb or more:
    data  11.1Mb
* 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 ... NOTE
runTopologyGSA,list : .local: no visible binding for global variable
  ‘expr’
runTopologyGSA,list : .local: no visible binding for global variable
  ‘classes’
* 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 32 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 ... [293s/298s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
runClipperMulti 233.111  4.049 237.353
runClipper       26.967  0.526  27.511
runSPIA           9.473  0.105  12.588
* 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: 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.1-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
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘plot’ from package ‘graphics’ in package ‘graphite’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
* DONE (graphite)

name	user	system	elapsed
as.list.DeprecatedPathwayList	2.491	0.360	2.854
as.list.PathwayList	0.211	0.034	0.245
convertIdentifiers	1.110	0.025	1.135
cytoscapePlot	0.001	0.000	0.001
pathwayDatabases	0.041	0.003	0.045
pathwayGraph	0.044	0.001	0.045
pathways	0.001	0.000	0.001
runClipper	26.967	0.526	27.511
runClipperMulti	233.111	4.049	237.353
runDEGraph	2.778	0.122	3.294
runDEGraphMulti	1.335	0.016	1.351
runSPIA	9.473	0.105	12.588
runTopologyGSA	2.424	0.036	3.649
runTopologyGSAMulti	1.388	0.033	1.927