Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-01-25 11:06:48 -0500 (Tue, 25 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4164
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4059
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2021-12-21 r81400 ucrt) -- "Unsuffered Consequences" 4001
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4118
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 biomaRt on riesling1


To the developers/maintainers of the biomaRt package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/biomaRt.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 179/2075HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
biomaRt 2.51.2  (landing page)
Mike Smith
Snapshot Date: 2022-01-24 13:55:18 -0500 (Mon, 24 Jan 2022)
git_url: https://git.bioconductor.org/packages/biomaRt
git_branch: master
git_last_commit: 0d887b7
git_last_commit_date: 2022-01-12 04:45:01 -0500 (Wed, 12 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  UNNEEDED, same version is already published

Summary

Package: biomaRt
Version: 2.51.2
Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:biomaRt.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings biomaRt_2.51.2.tar.gz
StartedAt: 2022-01-24 18:21:37 -0500 (Mon, 24 Jan 2022)
EndedAt: 2022-01-24 18:23:58 -0500 (Mon, 24 Jan 2022)
EllapsedTime: 140.8 seconds
RetCode: 0
Status:   OK  
CheckDir: biomaRt.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:biomaRt.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings biomaRt_2.51.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/biomaRt.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 'biomaRt/DESCRIPTION' ... OK
* this is package 'biomaRt' version '2.51.2'
* 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 'biomaRt' 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
* 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 ... NOTE
Unexported object imported by a ':::' call: 'AnnotationDbi:::smartKeys'
  See the note in ?`:::` about the use of this operator.
* 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 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/biomaRt.Rcheck/00check.log'
for details.



Installation output

biomaRt.Rcheck/00install.out

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


* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'biomaRt' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'biomaRt'
    finding HTML links ... done
    Mart-class                              html  
    NP2009code                              html  
    attributePages                          html  
    biomaRt-deprecated                      html  
    biomartCache                            html  
    exportFASTA                             html  
    filterType                              html  
    getBM                                   html  
    getGene                                 html  
    getLDS                                  html  
    getSequence                             html  
    listAttributes                          html  
    listDatasets                            html  
    listEnsembl                             html  
    listEnsemblArchives                     html  
    listFilterValues                        html  
    listFilters                             html  
    listMarts                               html  
    select                                  html  
    useDataset                              html  
    useEnsembl                              html  
    useMart                                 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 (biomaRt)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'HIPPO' is missing or broken
Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'scuttle' is missing or broken
 done

Tests output

biomaRt.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(mockery)
> library(biomaRt)
> 
> test_check("biomaRt", encoding = "UTF-8")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 144 ]
> 
> proc.time()
   user  system elapsed 
  14.34    0.62   45.43 

Example timings

biomaRt.Rcheck/biomaRt-Ex.timings

nameusersystemelapsed
NP2009code000
attributePages000
exportFASTA000
filterType000
getBM000
getGene000
getLDS000
getSequence000
listAttributes000
listDatasets000
listEnsembl000
listEnsemblArchives0.060.020.53
listFilterValues000
listFilters000
listMarts000
select000
useDataset000
useEnsembl000
useMart000