Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-01-21 11:07:25 -0500 (Fri, 21 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4163
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4058
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2021-12-21 r81400 ucrt) -- "Unsuffered Consequences" 4000
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4117
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for DOSE on riesling1


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 538/2075HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DOSE 3.21.2  (landing page)
Guangchuang Yu
Snapshot Date: 2022-01-20 13:55:17 -0500 (Thu, 20 Jan 2022)
git_url: https://git.bioconductor.org/packages/DOSE
git_branch: master
git_last_commit: 20c57bc
git_last_commit_date: 2022-01-04 01:56:36 -0500 (Tue, 04 Jan 2022)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  NO, package depends on 'AnnotationDbi' which is not available
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  NO, package depends on 'fgsea' which is not available

Summary

Package: DOSE
Version: 3.21.2
Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:DOSE.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings DOSE_3.21.2.tar.gz
StartedAt: 2022-01-20 18:45:35 -0500 (Thu, 20 Jan 2022)
EndedAt: 2022-01-20 18:48:17 -0500 (Thu, 20 Jan 2022)
EllapsedTime: 161.6 seconds
RetCode: 0
Status:   OK  
CheckDir: DOSE.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:DOSE.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings DOSE_3.21.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/DOSE.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* 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 '3.21.2'
* 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
* 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 ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  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
  'D:/biocbuild/bbs-3.15-bioc/meat/DOSE.Rcheck/00check.log'
for details.



Installation output

DOSE.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL DOSE
###
##############################################################################
##############################################################################


* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* 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
* DONE (DOSE)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'tenXplore' is missing or broken
Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'tRNA' is missing or broken
 done

Tests output

DOSE.Rcheck/tests/testthat.Rout


R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
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 v3.21.2  For help: https://yulab-smu.top/biomedical-knowledge-mining-book/

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 
   6.98    0.56    7.53 

Example timings

DOSE.Rcheck/DOSE-Ex.timings

nameusersystemelapsed
clusterSim0.860.000.86
enrichDO0.810.030.84
geneID0.830.100.92
geneInCategory0.460.070.55
mclusterSim0.380.070.44
theme_dose0.220.010.23