BioC 3.2: CHECK report for KEGGREST on oaxaca

Package: KEGGREST

Version: 1.9.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings KEGGREST_1.9.0.tar.gz

StartedAt: 2015-08-24 01:10:35 -0700 (Mon, 24 Aug 2015)

EndedAt: 2015-08-24 01:17:05 -0700 (Mon, 24 Aug 2015)

EllapsedTime: 390.3 seconds

RetCode: 1

Status:  ERROR

CheckDir: KEGGREST.Rcheck

Warnings: NA

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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_1.9.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/KEGGREST.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘KEGGREST/DESCRIPTION’ ... OK
* this is package ‘KEGGREST’ version ‘1.9.0’
* 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 ... [8s/9s] 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 ... [20s/135s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
keggList      5.784  0.970  26.008
listDatabases 5.367  0.955  21.530
keggConv      1.148  0.011  13.404
keggLink      0.665  0.155  34.629
keggFind      0.099  0.010  27.180
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘KEGGREST_unit_tests.R’ [13s/118s]
 ERROR
Running the tests in ‘tests/KEGGREST_unit_tests.R’ failed.
Last 13 lines of output:
  FAILURE in test_keggLink: Error in checkTrue(length(res) > 0) : Test not TRUE
  
  
  Test files with failing tests
  
     test_KEGGREST.R 
       test_keggConv 
       test_keggLink 
  
  
  Error in BiocGenerics:::testPackage("KEGGREST") : 
    unit tests failed for package KEGGREST
  Execution halted
* 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 ERROR, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.2-bioc/meat/KEGGREST.Rcheck/00check.log’
for details.

R version 3.2.2 (2015-08-14) -- "Fire Safety"
Copyright (C) 2015 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin13.4.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> BiocGenerics:::testPackage("KEGGREST")
Timing stopped at: 0.028 0.002 10.464 
Error in checkTrue(length(res) > 0) : Test not TRUE

Timing stopped at: 0.158 0.006 31.981 
Error in checkTrue(length(res) > 0) : Test not TRUE



RUNIT TEST PROTOCOL -- Mon Aug 24 01:16:50 2015 
*********************************************** 
Number of test functions: 10 
Number of errors: 0 
Number of failures: 2 

 
1 Test Suite : 
KEGGREST RUnit Tests - 10 test functions, 0 errors, 2 failures
FAILURE in test_keggConv: Error in checkTrue(length(res) > 0) : Test not TRUE

FAILURE in test_keggLink: Error in checkTrue(length(res) > 0) : Test not TRUE


Test files with failing tests

   test_KEGGREST.R 
     test_keggConv 
     test_keggLink 


Error in BiocGenerics:::testPackage("KEGGREST") : 
  unit tests failed for package KEGGREST
Execution halted

* 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	1.148	0.011	13.404
keggFind	0.099	0.010	27.180
keggGet	1.023	0.031	2.855
keggInfo	0.036	0.000	0.841
keggLink	0.665	0.155	34.629
keggList	5.784	0.970	26.008
listDatabases	5.367	0.955	21.530
mark.pathway.by.objects	0.093	0.005	4.275