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CHECK report for ClusterJudge on tokay1

This page was generated on 2020-04-15 12:28:42 -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: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ClusterJudge.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings ClusterJudge_1.8.0.tar.gz
StartedAt: 2020-04-15 02:07:54 -0400 (Wed, 15 Apr 2020)
EndedAt: 2020-04-15 02:14:01 -0400 (Wed, 15 Apr 2020)
EllapsedTime: 366.8 seconds
RetCode: 1
Status:  ERROR  
CheckDir: ClusterJudge.Rcheck
Warnings: NA

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ClusterJudge.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings ClusterJudge_1.8.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/ClusterJudge.Rcheck'
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... 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://downloads.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
Calls: download_Yeast_GO_mapping -> read.table -> textConnection -> readLines
Execution halted
** running examples for arch 'x64' ... 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://downloads.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
Calls: download_Yeast_GO_mapping -> read.table -> textConnection -> readLines
Execution halted
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  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: 2 ERRORs
See
  'C:/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:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/ClusterJudge_1.8.0.tar.gz && rm -rf ClusterJudge.buildbin-libdir && mkdir ClusterJudge.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ClusterJudge.buildbin-libdir ClusterJudge_1.8.0.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL ClusterJudge_1.8.0.zip && rm ClusterJudge_1.8.0.tar.gz ClusterJudge_1.8.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  799k  100  799k    0     0  17.9M      0 --:--:-- --:--:-- --:--:-- 19.5M

install for i386

* 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
  converting help for package 'ClusterJudge'
    finding HTML links ... done
    ClusterJudge-package                    html  
    Yeast.GO.assocs                         html  
    attribute_mut_inf                       html  
    clusterJudge                            html  
    clusterJudge_z_score                    html  
    consolidate_entity_attribute            html  
    convert_Yeast_SGDId_2_systematic        html  
    download_Yeast_GO_mapping               html  
    download_Yeast_Go_terms                 html  
    entities_attribute_stats                html  
    mi.GO.Yeast                             html  
    validate_association                    html  
** 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

install for x64

* installing *source* package 'ClusterJudge' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ClusterJudge' as ClusterJudge_1.8.0.zip
* DONE (ClusterJudge)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'ClusterJudge' successfully unpacked and MD5 sums checked

Tests output

ClusterJudge.Rcheck/tests_i386/testthat.Rout


R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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 
   1.00    0.06    1.04

ClusterJudge.Rcheck/tests_x64/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-w64-mingw32/x64 (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 
   1.32    0.10    1.42

Example timings

ClusterJudge.Rcheck/examples_i386/ClusterJudge-Ex.timings

nameusersystemelapsed
Yeast.GO.assocs0.050.020.07
attribute_mut_inf1.480.031.51
clusterJudge53.27 2.4555.72
clusterJudge_z_score38.31 0.6638.96
consolidate_entity_attribute57.31 0.9258.24
convert_Yeast_SGDId_2_systematic0.080.010.75

ClusterJudge.Rcheck/examples_x64/ClusterJudge-Ex.timings

nameusersystemelapsed
Yeast.GO.assocs0.060.030.10
attribute_mut_inf2.250.062.31
clusterJudge45.72 1.1246.86
clusterJudge_z_score40.08 0.5340.61
consolidate_entity_attribute77.90 0.8878.85
convert_Yeast_SGDId_2_systematic0.030.020.58