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CHECK report for ClusterJudge on merida1

This page was generated on 2020-04-15 12:45:40 -0400 (Wed, 15 Apr 2020).

Package 309/1823HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ClusterJudge 1.8.0
Adrian Pasculescu
Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/ClusterJudge
Branch: RELEASE_3_10
Last Commit: d806ac3
Last Changed Date: 2019-10-29 13:10:32 -0400 (Tue, 29 Oct 2019)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  ERROR 
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  ERROR  OK 
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK [ ERROR ] OK 

Summary

Package: ClusterJudge
Version: 1.8.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ClusterJudge.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ClusterJudge_1.8.0.tar.gz
StartedAt: 2020-04-15 01:16:34 -0400 (Wed, 15 Apr 2020)
EndedAt: 2020-04-15 01:20:38 -0400 (Wed, 15 Apr 2020)
EllapsedTime: 243.9 seconds
RetCode: 1
Status:  ERROR 
CheckDir: ClusterJudge.Rcheck
Warnings: NA

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ClusterJudge.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ClusterJudge_1.8.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/ClusterJudge.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ClusterJudge/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ClusterJudge’ version ‘1.8.0’
* 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 ‘ClusterJudge’ 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘ClusterJudge-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: download_Yeast_GO_mapping
> ### Title: downloads the Gene Ontology attributes mapped to Yeast genes
> ### Aliases: download_Yeast_GO_mapping
> 
> ### ** Examples
> 
> 
> Yeast.GO.assocs <- download_Yeast_GO_mapping()
Warning in readLines(gzcon(url(yeast.GO.url))) :
  cannot open URL 'http://sgd-archive.yeastgenome.org/curation/literature/gene_association.sgd.gz': HTTP status was '404 Not Found'
Error in readLines(gzcon(url(yeast.GO.url))) : 
  cannot open the connection to 'http://downloads.yeastgenome.org/curation/literature/gene_association.sgd.gz'
Calls: download_Yeast_GO_mapping -> read.table -> textConnection -> readLines
Execution halted
* 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: 1 ERROR
See
  ‘/Users/biocbuild/bbs-3.10-bioc/meat/ClusterJudge.Rcheck/00check.log’
for details.

Installation output

ClusterJudge.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL ClusterJudge
###
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##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘ClusterJudge’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** byte-compile and prepare package for lazy loading
** 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 (ClusterJudge)

Tests output

ClusterJudge.Rcheck/tests/testthat.Rout


R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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.

> library(testthat)
> library(ClusterJudge)
Loading required package: infotheo
Loading required package: lattice
Loading required package: latticeExtra
Loading required package: httr
Loading required package: jsonlite
> 
> test_check("ClusterJudge")
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 2 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  1.653   0.138   1.779

Example timings

ClusterJudge.Rcheck/ClusterJudge-Ex.timings

nameusersystemelapsed
Yeast.GO.assocs0.0560.0100.068
attribute_mut_inf2.2440.0862.351
clusterJudge64.505 2.37167.462
clusterJudge_z_score53.381 1.84055.724
consolidate_entity_attribute76.956 2.30480.351
convert_Yeast_SGDId_2_systematic0.4760.0091.254