BioC 3.1: CHECK report for gage on petty

Package: gage

Version: 2.18.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings gage_2.18.0.tar.gz

StartedAt: 2015-10-08 23:05:57 -0700 (Thu, 08 Oct 2015)

EndedAt: 2015-10-08 23:09:00 -0700 (Thu, 08 Oct 2015)

EllapsedTime: 182.7 seconds

RetCode: 0

Status:  OK

CheckDir: gage.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 gage_2.18.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/gage.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 ‘gage/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘gage’ version ‘2.18.0’
* 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 ‘gage’ can be installed ... [15s/15s] 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 ... NOTE
'library' or 'require' call to ‘GO.db’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
deComp: no visible global function definition for ‘annot.db’
eg2sym: no visible binding for global variable ‘egSymb’
esset.grp: no visible global function definition for ‘nodes’
esset.grp: no visible global function definition for ‘edgeNames’
esset.grp: no visible global function definition for ‘make.graph’
esset.grp : <anonymous>: no visible global function definition for
  ‘nodes’
go.gsets: no visible global function definition for ‘biocLite’
go.gsets: no visible binding for global variable ‘GOTERM’
kegg.gsets: no visible binding for global variable ‘khier’
kegg.species.code: no visible binding for global variable ‘korg’
sym2eg: no visible binding for global variable ‘egSymb’
* 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 files in ‘vignettes’ ... OK
* checking examples ... [31s/36s] OK
Examples with CPU or elapsed time > 5s
            user system elapsed
kegg.gsets 1.174  0.059   5.723
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.1-bioc/meat/gage.Rcheck/00check.log’
for details.

* installing *source* package ‘gage’ ...
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
** 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 (gage)

name	user	system	elapsed
eg2sym	1.936	0.118	2.054
egSymb	1.906	0.130	2.037
essGene	0.608	0.032	0.653
esset.grp	2.972	0.108	3.083
gage	4.562	0.182	4.749
gageComp	1.981	0.137	2.225
gagePipe	1.957	0.118	2.085
geneData	0.423	0.033	0.469
go.gsets	0.005	0.001	0.006
gs.tTest	0.418	0.025	0.443
gse16873	0.472	0.025	0.498
heter.gage	1.447	0.069	1.519
kegg.gs	2.071	0.150	2.221
kegg.gsets	1.174	0.059	5.723
readExpData	0.015	0.001	0.016
readList	0.315	0.017	0.334
sigGeneSet	1.015	0.054	1.076