BioC 2.14: CHECK report for FGNet on petty

Package: FGNet

Version: 2.0.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch FGNet_2.0.0.tar.gz

StartedAt: 2014-10-07 21:54:55 -0700 (Tue, 07 Oct 2014)

EndedAt: 2014-10-07 21:58:11 -0700 (Tue, 07 Oct 2014)

EllapsedTime: 195.8 seconds

RetCode: 0

Status:  OK

CheckDir: FGNet.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 FGNet_2.0.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/FGNet.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘FGNet/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘FGNet’ version ‘2.0.0’
* 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 ‘FGNet’ can be installed ... [5s/5s] 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
':::' call which should be '::': ‘RCurl:::parseHTTPHeader’
  See the note in ?`:::` about the use of this operator.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of 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
plotMetagroupsDistance: no visible global function definition for
  ‘brewer.pal’
query_david: no visible binding for global variable ‘DAVIDWebService’
query_david: no visible global function definition for ‘addList’
query_david : <anonymous>: no visible global function definition for
  ‘getIdTypes’
query_david: no visible global function definition for
  ‘setAnnotationCategories’
query_david : <anonymous>: no visible global function definition for
  ‘getAllAnnotationCategoryNames’
query_david: no visible global function definition for
  ‘getClusterReportFile’
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [54s/82s] OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
functionalNetwork      17.006  8.992  36.228
toMatrix                4.922  4.216  12.785
getResults_david        7.491  1.259  10.251
intersectionNetwork     1.967  1.920   7.640
getResults_gtLinker     1.654  1.507   6.321
plotMetagroupsDistance  0.250  0.077   5.788
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘runTests.R’ [3s/34s]
 [4s/34s] 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

NOTE: There were 2 notes.
See
  ‘/Users/biocbuild/bbs-2.14-bioc/meat/FGNet.Rcheck/00check.log’
for details.

* installing *source* package ‘FGNet’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (FGNet)

name	user	system	elapsed
FGNet-package	0.002	0.000	0.003
functionalNetwork	17.006	8.992	36.228
getResults_david	7.491	1.259	10.251
getResults_gtLinker	1.654	1.507	6.321
getTerms	0.001	0.000	0.002
intersectionNetwork	1.967	1.920	7.640
plotMetagroupsDistance	0.250	0.077	5.788
query_david	0.002	0.000	0.003
query_gtLinker	0.002	0.000	0.002
report	0.004	0.000	0.004
toMatrix	4.922	4.216	12.785