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CHECK report for ClusterJudge on tokay2

This page was generated on 2020-10-17 11:56:19 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE ClusterJudge PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 318/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ClusterJudge 1.10.0
Adrian Pasculescu
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/ClusterJudge
Branch: RELEASE_3_11
Last Commit: cc67203
Last Changed Date: 2020-04-27 15:08:42 -0400 (Mon, 27 Apr 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: ClusterJudge
Version: 1.10.0
Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ClusterJudge.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings ClusterJudge_1.10.0.tar.gz
StartedAt: 2020-10-17 02:42:14 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 02:49:49 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 455.0 seconds
RetCode: 0
Status:  OK  
CheckDir: ClusterJudge.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ClusterJudge.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings ClusterJudge_1.10.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/ClusterJudge.Rcheck'
* using R version 4.0.3 (2020-10-10)
* 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 '1.10.0'
* 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' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                              user system elapsed
consolidate_entity_attribute 66.48   1.16   67.64
download_Yeast_Go_terms      36.57   9.45   46.32
clusterJudge                 41.33   2.06   43.48
clusterJudge_z_score         39.83   0.58   40.41
download_Yeast_GO_mapping     5.75   0.07    6.47
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                              user system elapsed
clusterJudge                 58.28   1.50   59.78
consolidate_entity_attribute 57.41   1.06   58.47
clusterJudge_z_score         40.07   0.81   40.89
download_Yeast_Go_terms      20.14  10.31   30.67
download_Yeast_GO_mapping     5.83   0.10    6.55
* 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: OK


Installation output

ClusterJudge.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/ClusterJudge_1.10.0.tar.gz && rm -rf ClusterJudge.buildbin-libdir && mkdir ClusterJudge.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ClusterJudge.buildbin-libdir ClusterJudge_1.10.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL ClusterJudge_1.10.0.zip && rm ClusterJudge_1.10.0.tar.gz ClusterJudge_1.10.0.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  798k  100  798k    0     0  12.8M      0 --:--:-- --:--:-- --:--:-- 14.7M

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_1.10.0.zip
* DONE (ClusterJudge)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'ClusterJudge' successfully unpacked and MD5 sums checked

Tests output

ClusterJudge.Rcheck/tests_i386/testthat.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
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 
   1.53    0.12    1.64 

ClusterJudge.Rcheck/tests_x64/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-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 
   1.43    0.14    1.56 

Example timings

ClusterJudge.Rcheck/examples_i386/ClusterJudge-Ex.timings

nameusersystemelapsed
Yeast.GO.assocs0.060.030.09
attribute_mut_inf1.700.112.08
clusterJudge41.33 2.0643.48
clusterJudge_z_score39.83 0.5840.41
consolidate_entity_attribute66.48 1.1667.64
convert_Yeast_SGDId_2_systematic0.100.010.76
download_Yeast_GO_mapping5.750.076.47
download_Yeast_Go_terms36.57 9.4546.32
entities_attribute_stats0.190.000.18
mi.GO.Yeast0.220.050.27
validate_association0.120.010.14

ClusterJudge.Rcheck/examples_x64/ClusterJudge-Ex.timings

nameusersystemelapsed
Yeast.GO.assocs0.080.010.09
attribute_mut_inf2.440.102.75
clusterJudge58.28 1.5059.78
clusterJudge_z_score40.07 0.8140.89
consolidate_entity_attribute57.41 1.0658.47
convert_Yeast_SGDId_2_systematic0.060.000.67
download_Yeast_GO_mapping5.830.106.55
download_Yeast_Go_terms20.1410.3130.67
entities_attribute_stats0.080.000.08
mi.GO.Yeast0.160.020.17
validate_association0.120.010.14