BioC 3.4: CHECK report for rols on malbec1

Package: rols

Version: 2.2.5

Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings rols_2.2.5.tar.gz

StartedAt: 2017-04-15 01:02:09 -0400 (Sat, 15 Apr 2017)

EndedAt: 2017-04-15 01:09:43 -0400 (Sat, 15 Apr 2017)

EllapsedTime: 454.5 seconds

RetCode: 1

Status:  ERROR

CheckDir: rols.Rcheck

Warnings: NA

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### Running command:
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###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings rols_2.2.5.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/rols.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘rols/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘rols’ version ‘2.2.5’
* 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 ‘rols’ can be installed ... 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 ... OK
* 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 ... OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
Term-class       63.228  0.332 188.673
Properties-class  1.356  0.012   6.081
CVParam-class     1.144  0.020  13.978
OlsSearch-class   0.312  0.012   5.254
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  Testing term SO:0001068 
  Testing term SO:1001262 
  Testing term SO:1000058 
  Testing term SO:0001147 
  Testing term SO:1000183 
  Testing term SO:0000907 
  Testing term SO:0001647 
  Testing term SO:1001266 
  Testing term SO:0001329 
  testthat results ================================================================
  OK: 194 SKIPPED: 0 FAILED: 1
  1. Error: unique terms (@test_Terms.R#109) 
  
  Error: testthat unit tests failed
  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
See
  ‘/home/biocbuild/bbs-3.4-bioc/meat/rols.Rcheck/00check.log’
for details.

R version 3.3.3 (2017-03-06) -- "Another Canoe"
Copyright (C) 2017 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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.

> # setting R_TESTS to empty string because of 
> # https://github.com/hadley/testthat/issues/144
> # revert this when that issue in R is fixed.
> Sys.setenv("R_TESTS" = "")
> library("testthat")
> library("rols")

This is 'rols' version 2.2.5 

> 
> test_check("rols")
[, , Hello, World] 
Object of class 'OlsSearch':
  ontolgy: GO 
  query: cell 
  requested: 20 (out of 10124)
  response(s): 0 
Object of class 'Ontologies' with 166 entries
   AERO, CMO ... ZFA, ZFS 
Object of class 'Ontologies' with 1 entries
AERO 
Object of class 'Ontologies' with 2 entries
AERO, CMO 
Object of class 'Ontologies' with 3 entries
AERO, CMO, CMPO 
Object of class 'Ontologies' with 4 entries
AERO, CMO, CMPO, CTENO 
Object of class 'Ontologies' with 5 entries
   AERO, CMO ... CTENO, CVDO 
Ontology: Gene Ontology (go)  
  An ontology for describing the function of genes and gene products
   Loaded: 2017-04-14 Updated: 2017-04-14 Version: 2017-04-12 
   48560 terms  68 properties  0 individuals
Object of class 'Properties' with 89 entries
 From the SO ontology
  partial_evidence_for_feature, evidence_for_feature ... variant_of, DBVAR 
Object of class 'Properties' with 444 entries
 From the UBERON ontology
  exocrine gland, endoderm-derived structure ... liver bud, septum transversum 
A Property from the UBERON ontology: UBERON:0002365 
 Label: exocrine gland
Object of class 'Terms' with 2378 entries
 From the SO ontology
  SO:0000579, SO:0000833 ... SO:0000071, SO:0000070 
Object of class 'Terms' with 1 entries
 From the SO ontology
SO:0000579 
Object of class 'Terms' with 2 entries
 From the SO ontology
SO:0000579, SO:0000833 
Object of class 'Terms' with 3 entries
 From the SO ontology
SO:0000579, SO:0000833, SO:0000578 
Object of class 'Terms' with 4 entries
 From the SO ontology
SO:0000579, SO:0000833, SO:0000578, SO:0000011 
Object of class 'Terms' with 5 entries
 From the SO ontology
  SO:0000579, SO:0000833 ... SO:0000011, SO:0000577 
A Term from the GO ontology: GO:0032801 
 Label: receptor catabolic process
  The chemical reactions and pathways resulting in the breakdown of a
  receptor molecule, a macromolecule that undergoes combination with a
  hormone, neurotransmitter, drug or intracellular messenger to initiate
  a change in cell function.
1. Error: unique terms (@test_Terms.R#109) -------------------------------------
Not Found (HTTP 404).
1: term("nbo", "GO:0005802") at testthat/test_Terms.R:109
2: term("nbo", "GO:0005802")
3: .term(object, id, ...)
4: stop_for_status(x)

Testing term SO:0000383 
Testing term SO:0001068 
Testing term SO:1001262 
Testing term SO:1000058 
Testing term SO:0001147 
Testing term SO:1000183 
Testing term SO:0000907 
Testing term SO:0001647 
Testing term SO:1001266 
Testing term SO:0001329 
testthat results ================================================================
OK: 194 SKIPPED: 0 FAILED: 1
1. Error: unique terms (@test_Terms.R#109) 

Error: testthat unit tests failed
Execution halted

* installing *source* package ‘rols’ ...
** R
** inst
** preparing package for lazy loading
Creating a generic function for ‘lapply’ from package ‘base’ in package ‘rols’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (rols)

name	user	system	elapsed
CVParam-class	1.144	0.020	13.978
OlsSearch-class	0.312	0.012	5.254
Ontology-class	0.400	0.008	3.138
Properties-class	1.356	0.012	6.081
Term-class	63.228	0.332	188.673