BioC 3.1: CHECK report for KEGGREST on petty

Package: KEGGREST

Version: 1.8.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings KEGGREST_1.8.1.tar.gz

StartedAt: 2015-10-08 23:55:33 -0700 (Thu, 08 Oct 2015)

EndedAt: 2015-10-09 00:02:15 -0700 (Fri, 09 Oct 2015)

EllapsedTime: 402.2 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 KEGGREST_1.8.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/KEGGREST.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 ‘KEGGREST/DESCRIPTION’ ... OK
* this is package ‘KEGGREST’ version ‘1.8.1’
* 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 ... [11s/11s] 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.
* 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 ... [34s/149s] OK
Examples with CPU or elapsed time > 5s
                user system elapsed
listDatabases 10.217  1.993  22.713
keggList      10.192  1.926  24.691
keggLink       1.917  0.458  38.990
keggConv       0.201  0.021  20.820
keggFind       0.159  0.014  27.004
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘KEGGREST_unit_tests.R’ [19s/133s]
 [20s/133s] 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
* DONE

Status: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.1-bioc/meat/KEGGREST.Rcheck/00check.log’
for details.

* installing *source* package ‘KEGGREST’ ...
** R
** 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 (KEGGREST)

name	user	system	elapsed
keggConv	0.201	0.021	20.820
keggFind	0.159	0.014	27.004
keggGet	1.568	0.053	3.616
keggInfo	0.054	0.001	0.930
keggLink	1.917	0.458	38.990
keggList	10.192	1.926	24.691
listDatabases	10.217	1.993	22.713
mark.pathway.by.objects	0.078	0.014	4.609