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This page was generated on 2021-07-30 15:05:51 -0400 (Fri, 30 Jul 2021).

CHECK results for DOSE on tokay2

To the developers/maintainers of the DOSE package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/DOSE.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 528/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DOSE 3.18.1  (landing page)
Guangchuang Yu
Snapshot Date: 2021-07-29 04:50:02 -0400 (Thu, 29 Jul 2021)
URL: https://git.bioconductor.org/packages/DOSE
Branch: RELEASE_3_13
Last Commit: c971ee2
Last Changed Date: 2021-06-20 22:17:47 -0400 (Sun, 20 Jun 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: DOSE
Version: 3.18.1
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:DOSE.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings DOSE_3.18.1.tar.gz
StartedAt: 2021-07-29 22:47:13 -0400 (Thu, 29 Jul 2021)
EndedAt: 2021-07-29 22:51:12 -0400 (Thu, 29 Jul 2021)
EllapsedTime: 238.9 seconds
RetCode: 0
Status:   OK  
CheckDir: DOSE.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:DOSE.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings DOSE_3.18.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/DOSE.Rcheck'
* using R version 4.1.0 (2021-05-18)
* 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 '3.18.1'
* package encoding: UTF-8
* 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 'DOSE' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data   6.0Mb
* 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: 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.13-bioc/meat/DOSE.Rcheck/00check.log'
for details.



Installation output

DOSE.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/DOSE_3.18.1.tar.gz && rm -rf DOSE.buildbin-libdir && mkdir DOSE.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=DOSE.buildbin-libdir DOSE_3.18.1.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL DOSE_3.18.1.zip && rm DOSE_3.18.1.tar.gz DOSE_3.18.1.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
 16 6150k   16 1042k    0     0  2997k      0  0:00:02 --:--:--  0:00:02 2996k
100 6150k  100 6150k    0     0  4791k      0  0:00:01  0:00:01 --:--:-- 4794k

install for i386

* installing *source* package 'DOSE' ...
** using staged installation
** 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  
    compareClusterResult-class              html  
    computeIC                               html  
    doSim                                   html  
    enrichDGN                               html  
    enrichDGNv                              html  
    enrichDO                                html  
    enrichNCG                               html  
    enrichResult-class                      html  
    enricher_internal                       html  
    gene2DO                                 html  
    geneID                                  html  
    geneInCategory                          html  
    geneSim                                 html  
    gseDGN                                  html  
    gseDO                                   html  
    gseNCG                                  html  
    gseaResult-class                        html  
    gsfilter                                html  
    mclusterSim                             html  
    parse_ratio                             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 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 'DOSE' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'DOSE' as DOSE_3.18.1.zip
* DONE (DOSE)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'DOSE' successfully unpacked and MD5 sums checked

Tests output

DOSE.Rcheck/tests_i386/testthat.Rout


R version 4.1.0 (2021-05-18) -- "Camp Pontanezen"
Copyright (C) 2021 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 v3.18.1  For help: https://guangchuangyu.github.io/software/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")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 3 ]
> 
> 
> proc.time()
   user  system elapsed 
   7.76    0.50    8.28 

DOSE.Rcheck/tests_x64/testthat.Rout


R version 4.1.0 (2021-05-18) -- "Camp Pontanezen"
Copyright (C) 2021 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 v3.18.1  For help: https://guangchuangyu.github.io/software/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")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 3 ]
> 
> 
> proc.time()
   user  system elapsed 
   7.65    0.29    7.93 

Example timings

DOSE.Rcheck/examples_i386/DOSE-Ex.timings

nameusersystemelapsed
clusterSim0.510.050.56
enrichDO0.860.050.91
geneID0.630.010.64
geneInCategory0.590.000.59
mclusterSim0.890.020.91
theme_dose0.160.010.17

DOSE.Rcheck/examples_x64/DOSE-Ex.timings

nameusersystemelapsed
clusterSim1.160.011.17
enrichDO1.230.021.25
geneID1.110.051.16
geneInCategory0.590.000.59
mclusterSim0.530.000.53
theme_dose0.20.00.2