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CHECK report for rols on merida1

This page was generated on 2019-04-16 11:56:21 -0400 (Tue, 16 Apr 2019).

Package 1339/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
rols 2.10.1
Laurent Gatto
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/rols
Branch: RELEASE_3_8
Last Commit: 6648d28
Last Changed Date: 2019-01-04 13:12:07 -0400 (Fri, 04 Jan 2019)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  ERROR 
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK [ ERROR ] OK 

Summary

Package: rols
Version: 2.10.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:rols.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings rols_2.10.1.tar.gz
StartedAt: 2019-04-16 02:28:11 -0400 (Tue, 16 Apr 2019)
EndedAt: 2019-04-16 02:38:57 -0400 (Tue, 16 Apr 2019)
EllapsedTime: 646.2 seconds
RetCode: 1
Status:  ERROR 
CheckDir: rols.Rcheck
Warnings: NA

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:rols.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings rols_2.10.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/rols.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘2.10.1’
* package encoding: UTF-8
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
Term-class       69.795  2.143 190.176
CVParam-class     1.375  0.048  30.664
Ontology-class    0.468  0.019   8.064
Properties-class  0.382  0.011   6.377
OlsSearch-class   0.282  0.013  13.586
* 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:1001274 
  Testing term SO:0000217 
  Testing term SO:0000172 
  Testing term SO:1000141 
  Testing term SO:0001881 
  Testing term SO:0002188 
  Testing term SO:0000255 
  Testing term SO:0001622 
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 2766 SKIPPED: 0 FAILED: 2
  1. Failure: accessors (@test_Terms.R#84) 
  2. Failure: accessors (@test_Terms.R#85) 
  
  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
  ‘/Users/biocbuild/bbs-3.8-bioc/meat/rols.Rcheck/00check.log’
for details.


Installation output

rols.Rcheck/00install.out

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL rols
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘rols’ ...
** R
** inst
** byte-compile and prepare 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)

Tests output

rols.Rcheck/tests/testthat.Rout.fail


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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.

> # 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 2.10.1 

> 
> test_check("rols")
[, , Hello, World] 
Object of class 'OlsSearch':
  ontolgy: GO 
  query: cell 
  requested: 20 (out of 10060)
  response(s): 0 
Object of class 'Ontologies' with 227 entries
   AEO, AERO ... TEDDY, TO 
Object of class 'Ontologies' with 1 entries
AEO 
Object of class 'Ontologies' with 2 entries
AEO, AERO 
Object of class 'Ontologies' with 3 entries
AEO, AERO, AGRO 
Object of class 'Ontologies' with 4 entries
AEO, AERO, AGRO, ancestro 
Object of class 'Ontologies' with 5 entries
   AEO, AERO ... ancestro, APO 
Ontology: Gene Ontology (go)  
  An ontology for describing the function of genes and gene products
   Loaded: 2019-03-20 Updated: 2019-04-15 Version: 2019-03-19 
   49801 terms  60 properties  0 individuals
Object of class 'Properties' with 90 entries
 From the SO ontology
  partial_evidence_for_feature, evidence_for_feature ... variant_of, DBVAR 
Object of class 'Properties' with 112 entries
 From the UBERON ontology
  digestive system gland, abdomen element ... bile, liver lobule 
A Property from the UBERON ontology: UBERON:0006925 
 Label: digestive system gland
Object of class 'Terms' with 2569 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:0001430 
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. Failure: accessors (@test_Terms.R#84)  ───────────────────────────────────
sum(isObsolete(trms)) not equal to `k`.
1/1 mismatches
[1] 335 - 204 == 131

── 2. Failure: accessors (@test_Terms.R#85)  ───────────────────────────────────
sum(!isObsolete(trms)) not equal to length(trms) - k.
1/1 mismatches
[1] 2234 - 2365 == -131

Testing term SO:0000591 
Testing term SO:0000489 
Testing term SO:1001274 
Testing term SO:0000217 
Testing term SO:0000172 
Testing term SO:1000141 
Testing term SO:0001881 
Testing term SO:0002188 
Testing term SO:0000255 
Testing term SO:0001622 
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 2766 SKIPPED: 0 FAILED: 2
1. Failure: accessors (@test_Terms.R#84) 
2. Failure: accessors (@test_Terms.R#85) 

Error: testthat unit tests failed
Execution halted

Example timings

rols.Rcheck/rols-Ex.timings

nameusersystemelapsed
CVParam-class 1.375 0.04830.664
OlsSearch-class 0.282 0.01313.586
Ontology-class0.4680.0198.064
Properties-class0.3820.0116.377
Term-class 69.795 2.143190.176