Back to Multiple platform build/check report for BioC 3.9
AB[C]DEFGHIJKLMNOPQRSTUVWXYZ

CHECK report for ClusterJudge on tokay2

This page was generated on 2019-04-09 12:31:42 -0400 (Tue, 09 Apr 2019).

Package 288/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ClusterJudge 1.5.0
Adrian Pasculescu
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/ClusterJudge
Branch: master
Last Commit: bbc907c
Last Changed Date: 2018-11-05 10:55:24 -0400 (Mon, 05 Nov 2018)
malbec2 Linux (Ubuntu 18.04.2 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
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  ERROR  skipped  skipped 
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK 

Summary

Package: ClusterJudge
Version: 1.5.0
Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ClusterJudge.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings ClusterJudge_1.5.0.tar.gz
StartedAt: 2019-04-09 01:50:21 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 01:56:32 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 370.8 seconds
RetCode: 0
Status:  OK  
CheckDir: ClusterJudge.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ClusterJudge.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings ClusterJudge_1.5.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/ClusterJudge.Rcheck'
* using R Under development (unstable) (2019-03-09 r76216)
* 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 '1.5.0'
* 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 or elapsed time > 5s
                              user system elapsed
consolidate_entity_attribute 49.51   0.80   50.31
clusterJudge                 44.70   2.20   46.90
clusterJudge_z_score         34.61   0.67   35.28
download_Yeast_Go_terms      18.79   0.04   19.13
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                              user system elapsed
consolidate_entity_attribute 54.63   0.98   55.64
clusterJudge                 51.41   1.22   52.62
clusterJudge_z_score         38.83   0.71   39.54
download_Yeast_Go_terms      16.70   0.16   17.11
* 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

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/ClusterJudge_1.5.0.tar.gz && rm -rf ClusterJudge.buildbin-libdir && mkdir ClusterJudge.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ClusterJudge.buildbin-libdir ClusterJudge_1.5.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL ClusterJudge_1.5.0.zip && rm ClusterJudge_1.5.0.tar.gz ClusterJudge_1.5.0.zip
###
##############################################################################
##############################################################################


  % 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  10.3M      0 --:--:-- --:--:-- --:--:-- 11.4M

install for i386

* installing *source* package 'ClusterJudge' ...
** 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_1.5.0.zip
* DONE (ClusterJudge)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'ClusterJudge' successfully unpacked and MD5 sums checked

Tests output

ClusterJudge.Rcheck/tests_i386/testthat.Rout


R Under development (unstable) (2019-03-09 r76216) -- "Unsuffered Consequences"
Copyright (C) 2019 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: RColorBrewer
Loading required package: httr
Loading required package: jsonlite
> 
> test_check("ClusterJudge")
== testthat results  ===========================================================
OK: 2 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
   0.68    0.12    0.79 

ClusterJudge.Rcheck/tests_x64/testthat.Rout


R Under development (unstable) (2019-03-09 r76216) -- "Unsuffered Consequences"
Copyright (C) 2019 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: RColorBrewer
Loading required package: httr
Loading required package: jsonlite
> 
> test_check("ClusterJudge")
== testthat results  ===========================================================
OK: 2 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
   0.68    0.09    0.76 

Example timings

ClusterJudge.Rcheck/examples_i386/ClusterJudge-Ex.timings

nameusersystemelapsed
Yeast.GO.assocs0.080.010.09
attribute_mut_inf1.590.041.64
clusterJudge44.7 2.246.9
clusterJudge_z_score34.61 0.6735.28
consolidate_entity_attribute49.51 0.8050.31
convert_Yeast_SGDId_2_systematic0.100.031.21
download_Yeast_GO_mapping3.310.054.18
download_Yeast_Go_terms18.79 0.0419.13
entities_attribute_stats0.180.000.17
mi.GO.Yeast0.250.030.28
validate_association0.140.000.14

ClusterJudge.Rcheck/examples_x64/ClusterJudge-Ex.timings

nameusersystemelapsed
Yeast.GO.assocs0.080.020.10
attribute_mut_inf2.500.092.59
clusterJudge51.41 1.2252.62
clusterJudge_z_score38.83 0.7139.54
consolidate_entity_attribute54.63 0.9855.64
convert_Yeast_SGDId_2_systematic0.040.001.27
download_Yeast_GO_mapping2.320.063.05
download_Yeast_Go_terms16.70 0.1617.11
entities_attribute_stats0.910.010.92
mi.GO.Yeast0.180.070.25
validate_association0.120.000.13