BioC 2.13: CHECK report for FGNet on perceval

Package: FGNet

Version: 1.2.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch FGNet_1.2.2.tar.gz

StartedAt: 2014-04-05 01:11:00 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 01:13:15 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 135.1 seconds

RetCode: 0

Status:  OK

CheckDir: FGNet.Rcheck

Warnings: 0

* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/FGNet.Rcheck’
* using R version 3.0.3 (2014-03-06)
* 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 ‘1.2.2’
* 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 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 ... [25s/65s] OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
functionalNetwork      4.598  1.706  18.823
getResults_david       5.547  0.449   8.152
report                 2.394  1.673   9.269
toMatrix               1.620  1.710   8.381
intersectionNetwork    0.849  0.794   7.094
plotMetagroupsDistance 0.203  0.081   5.539
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘runTests.R’ [3s/13s]
 [3s/13s] 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-2.13-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	0.014	0.001	0.014
functionalNetwork	4.598	1.706	18.823
getResults_david	5.547	0.449	8.152
getResults_gtLinker	0.095	0.061	4.753
getTerms	0.011	0.002	0.015
intersectionNetwork	0.849	0.794	7.094
plotMetagroupsDistance	0.203	0.081	5.539
query_david	0.013	0.002	0.015
query_gtLinker	0.012	0.002	0.013
report	2.394	1.673	9.269
toMatrix	1.620	1.710	8.381