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CHECK report for rols on machv2

This page was generated on 2020-10-17 11:59:27 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE rols PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1524/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
rols 2.16.4
Laurent Gatto
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/rols
Branch: RELEASE_3_11
Last Commit: 4525ecf
Last Changed Date: 2020-08-26 03:32:57 -0400 (Wed, 26 Aug 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: rols
Version: 2.16.4
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_2.16.4.tar.gz
StartedAt: 2020-10-17 04:48:13 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 05:00:18 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 725.2 seconds
RetCode: 0
Status:  OK 
CheckDir: rols.Rcheck
Warnings: 0

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_2.16.4.tar.gz
###
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##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/rols.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-apple-darwin17.0 (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 ‘2.16.4’
* 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 (user + system) or elapsed time > 5s
                  user system elapsed
Term-class      95.651  1.547 292.358
CVParam-class    0.820  0.038  19.052
Ontology-class   0.603  0.018   5.296
OlsSearch-class  0.346  0.015   7.554
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 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

Status: OK


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/4.0/Resources/library’
* installing *source* package ‘rols’ ...
** using staged installation
** 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 from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (rols)

Tests output

rols.Rcheck/tests/testthat.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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 2.16.4 

> 
> test_check("rols")
[, , Hello, World] 
Object of class 'OlsSearch':
  ontolgy: GO 
  query: cell 
  requested: 20 (out of 9829)
  response(s): 0 
Object of class 'Ontologies' with 252 entries
   AEO, AFO ... ZFA, ZP 
Object of class 'Ontologies' with 1 entries
AEO 
Object of class 'Ontologies' with 2 entries
AEO, AFO 
Object of class 'Ontologies' with 3 entries
AEO, AFO, AGRO 
Object of class 'Ontologies' with 4 entries
AEO, AFO, AGRO, AMPHX 
Object of class 'Ontologies' with 5 entries
   AEO, AFO ... AMPHX, APO 
Ontology: Gene Ontology (go)  
  The Gene Ontology (GO) provides a framework and set of concepts for
  describing the functions of gene products from all organisms.
   Loaded: 2020-10-14 Updated: 2020-10-16 Version: 2020-10-09 
   50422 terms  62 properties  0 individuals
Object of class 'Properties' with 92 entries
 From the SO ontology
  partial_evidence_for_feature, evidence_for_feature ... variant_of, DBVAR 
Object of class 'Properties' with 115 entries
 From the UBERON ontology
  digestive system gland, abdomen element ... liver lobule, bile 
A Property from the UBERON ontology: UBERON:0006925 
 Label: digestive system gland
Object of class 'Terms' with 2662 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.
Testing term SO:0000046 
Testing term SO:0001058 
Testing term SO:1001254 
Testing term SO:0001369 
Testing term SO:0000105 
Testing term SO:0000196 
Testing term SO:0001367 
Testing term SO:1000095 
Testing term SO:0001640 
Testing term SO:0001509 
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 2858 | SKIPPED: 0 | WARNINGS: 1 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
109.295   1.218 347.449 

Example timings

rols.Rcheck/rols-Ex.timings

nameusersystemelapsed
CVParam-class 0.820 0.03819.052
OlsSearch-class0.3460.0157.554
Ontology-class0.6030.0185.296
Properties-class0.4770.0104.483
Term-class 95.651 1.547292.358