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BioC 2.13: CHECK report for KEGGREST on perceval

This page was generated on 2014-04-05 09:53:01 -0700 (Sat, 05 Apr 2014).

Package 391/750HostnameOS / ArchBUILDCHECKBUILD BIN
KEGGREST 1.2.2
Bioconductor Package Maintainer
Snapshot Date: 2014-04-04 16:20:29 -0700 (Fri, 04 Apr 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/KEGGREST
Last Changed Rev: 87893 / Revision: 88450
Last Changed Date: 2014-03-25 16:41:25 -0700 (Tue, 25 Mar 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK [ OK ] OK 

Summary

Package: KEGGREST
Version: 1.2.2
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch KEGGREST_1.2.2.tar.gz
StartedAt: 2014-04-05 02:15:54 -0700 (Sat, 05 Apr 2014)
EndedAt: 2014-04-05 02:21:32 -0700 (Sat, 05 Apr 2014)
EllapsedTime: 337.8 seconds
RetCode: 0
Status:  OK 
CheckDir: KEGGREST.Rcheck
Warnings: 0

Command output

* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/KEGGREST.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 ‘KEGGREST/DESCRIPTION’ ... OK
* this is package ‘KEGGREST’ 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 ‘KEGGREST’ can be installed ... [13s/13s] 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.
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 ... [29s/103s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
listDatabases 6.838  1.126  16.343
keggList      6.696  1.098  17.914
keggLink      1.882  0.460  14.678
keggConv      0.779  0.103  18.505
keggFind      0.190  0.017  19.318
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘KEGGREST_unit_tests.R’ [22s/100s]
 [23s/100s] 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-2.13-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 0.779 0.10318.505
keggFind 0.190 0.01719.318
keggGet2.1440.0934.315
keggInfo0.0780.0100.963
keggLink 1.882 0.46014.678
keggList 6.696 1.09817.914
listDatabases 6.838 1.12616.343
mark.pathway.by.objects0.4060.0284.259