BioC 2.14: CHECK report for KEGGREST on petty

Package: KEGGREST

Version: 1.4.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch KEGGREST_1.4.1.tar.gz

StartedAt: 2014-10-07 22:40:57 -0700 (Tue, 07 Oct 2014)

EndedAt: 2014-10-07 22:47:33 -0700 (Tue, 07 Oct 2014)

EllapsedTime: 396.0 seconds

RetCode: 0

Status:  OK

CheckDir: KEGGREST.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 KEGGREST_1.4.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/KEGGREST.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 ‘KEGGREST/DESCRIPTION’ ... OK
* this is package ‘KEGGREST’ version ‘1.4.1’
* 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 ‘KEGGREST’ can be installed ... [14s/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
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Unexported object imported by a ':::' call: ‘BiocGenerics:::testPackage’
  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 ... OK
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [38s/123s] OK
Examples with CPU or elapsed time > 5s
                user system elapsed
listDatabases 10.184  1.496  20.103
keggList      10.142  1.460  22.519
keggLink       2.682  0.583  20.245
keggConv       1.475  0.137  21.276
keggFind       0.268  0.018  21.924
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘KEGGREST_unit_tests.R’ [30s/117s]
 [31s/118s] 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 was 1 note.
See
  ‘/Users/biocbuild/bbs-2.14-bioc/meat/KEGGREST.Rcheck/00check.log’
for details.

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

name	user	system	elapsed
keggConv	1.475	0.137	21.276
keggFind	0.268	0.018	21.924
keggGet	2.417	0.063	4.391
keggInfo	0.111	0.004	0.993
keggLink	2.682	0.583	20.245
keggList	10.142	1.460	22.519
listDatabases	10.184	1.496	20.103
mark.pathway.by.objects	0.105	0.013	4.112