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BioC 3.0: CHECK report for KEGGREST on perceval

This page was generated on 2015-04-10 09:57:42 -0700 (Fri, 10 Apr 2015).

Package 479/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
KEGGREST 1.6.4
Bioconductor Package Maintainer
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/KEGGREST
Last Changed Rev: 99617 / Revision: 102249
Last Changed Date: 2015-02-19 09:40:08 -0800 (Thu, 19 Feb 2015)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK [ OK ] OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK 

Summary

Package: KEGGREST
Version: 1.6.4
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch KEGGREST_1.6.4.tar.gz
StartedAt: 2015-04-10 03:05:48 -0700 (Fri, 10 Apr 2015)
EndedAt: 2015-04-10 03:11:59 -0700 (Fri, 10 Apr 2015)
EllapsedTime: 371.2 seconds
RetCode: 0
Status:  OK 
CheckDir: KEGGREST.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch KEGGREST_1.6.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/KEGGREST.Rcheck’
* using R version 3.1.3 (2015-03-09)
* 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 ‘1.6.4’
* 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 ... [13s/14s] 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 ... [28s/121s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
keggList      6.929  1.100  19.191
listDatabases 6.730  1.098  18.506
keggLink      1.659  0.435  18.505
keggConv      0.877  0.025  22.656
keggFind      0.175  0.021  26.037
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘KEGGREST_unit_tests.R’ [21s/114s]
 [21s/114s] 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

NOTE: There was 1 note.
See
  ‘/Users/biocbuild/bbs-3.0-bioc/meat/KEGGREST.Rcheck/00check.log’
for details.

KEGGREST.Rcheck/00install.out:

* 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)

KEGGREST.Rcheck/KEGGREST-Ex.timings:

nameusersystemelapsed
keggConv 0.877 0.02522.656
keggFind 0.175 0.02126.037
keggGet1.6810.0723.628
keggInfo0.0690.0040.962
keggLink 1.659 0.43518.505
keggList 6.929 1.10019.191
listDatabases 6.730 1.09818.506
mark.pathway.by.objects0.0680.0144.389