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CHECK report for DOSE on tokay1

This page was generated on 2019-04-13 11:21:40 -0400 (Sat, 13 Apr 2019).

Package 432/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DOSE 3.8.2
Guangchuang Yu
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/DOSE
Branch: RELEASE_3_8
Last Commit: 4d3d1ca
Last Changed Date: 2019-01-14 03:40:52 -0400 (Mon, 14 Jan 2019)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: DOSE
Version: 3.8.2
Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:DOSE.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings DOSE_3.8.2.tar.gz
StartedAt: 2019-04-13 01:53:20 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 01:57:11 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 231.2 seconds
RetCode: 0
Status:  OK  
CheckDir: DOSE.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:DOSE.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings DOSE_3.8.2.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/DOSE.Rcheck'
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'DOSE/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'DOSE' version '3.8.2'
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 'DOSE' 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
** running examples for arch 'x64' ... OK
* 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

DOSE.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/DOSE_3.8.2.tar.gz && rm -rf DOSE.buildbin-libdir && mkdir DOSE.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=DOSE.buildbin-libdir DOSE_3.8.2.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL DOSE_3.8.2.zip && rm DOSE_3.8.2.tar.gz DOSE_3.8.2.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 4515k  100 4515k    0     0  24.2M      0 --:--:-- --:--:-- --:--:-- 24.7M

install for i386

* installing *source* package 'DOSE' ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'DOSE'
    finding HTML links ... done
    DOSE-package                            html  
    DataSet                                 html  
    EXTID2NAME                              html  
    GSEA_internal                           html  
    clusterSim                              html  
    computeIC                               html  
    doSim                                   html  
    enrichDGN                               html  
    enrichDGNv                              html  
    enrichDO                                html  
    enrichNCG                               html  
    enrichResult-class                      html  
    enricher_internal                       html  
    fortify.enrichResult                    html  
    gene2DO                                 html  
    geneID                                  html  
    geneInCategory                          html  
    geneSim                                 html  
    gseDGN                                  html  
    gseDO                                   html  
    gseNCG                                  html  
    gseaResult-class                        html  
    gsfilter                                html  
    mclusterSim                             html  
    rebuildAnnoData                         html  
    reexports                               html  
    setReadable                             html  
    show-methods                            html  
    simplot                                 html  
    summary-methods                         html  
    theme_dose                              html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'DOSE' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'DOSE' as DOSE_3.8.2.zip
* DONE (DOSE)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'DOSE' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output

DOSE.Rcheck/tests_i386/testthat.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
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(DOSE)

DOSE v3.8.2  For help: https://guangchuangyu.github.io/DOSE

If you use DOSE in published research, please cite:
Guangchuang Yu, Li-Gen Wang, Guang-Rong Yan, Qing-Yu He. DOSE: an R/Bioconductor package for Disease Ontology Semantic and Enrichment analysis. Bioinformatics 2015, 31(4):608-609

> 
> test_check("DOSE")
== testthat results  ===========================================================
OK: 3 SKIPPED: 0 FAILED: 0
> 
> 
> proc.time()
   user  system elapsed 
   4.75    0.39    5.14 

DOSE.Rcheck/tests_x64/testthat.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
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(DOSE)

DOSE v3.8.2  For help: https://guangchuangyu.github.io/DOSE

If you use DOSE in published research, please cite:
Guangchuang Yu, Li-Gen Wang, Guang-Rong Yan, Qing-Yu He. DOSE: an R/Bioconductor package for Disease Ontology Semantic and Enrichment analysis. Bioinformatics 2015, 31(4):608-609

> 
> test_check("DOSE")
== testthat results  ===========================================================
OK: 3 SKIPPED: 0 FAILED: 0
> 
> 
> proc.time()
   user  system elapsed 
   5.45    0.29    5.73 

Example timings

DOSE.Rcheck/examples_i386/DOSE-Ex.timings

nameusersystemelapsed
clusterSim1.060.041.09
enrichDO1.140.171.31
geneID0.740.040.79
geneInCategory0.780.000.78
mclusterSim0.660.040.68
theme_dose0.210.000.22

DOSE.Rcheck/examples_x64/DOSE-Ex.timings

nameusersystemelapsed
clusterSim0.940.030.97
enrichDO1.280.001.28
geneID1.140.001.14
geneInCategory0.640.000.64
mclusterSim0.570.000.56
theme_dose0.210.000.22