Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-01-14 13:07:31 -0500 (Fri, 14 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4327
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4076
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4137
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 machv2


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 182/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
biomaRt 2.50.2  (landing page)
Mike Smith
Snapshot Date: 2022-01-13 01:55:04 -0500 (Thu, 13 Jan 2022)
git_url: https://git.bioconductor.org/packages/biomaRt
git_branch: RELEASE_3_14
git_last_commit: 9633bbd
git_last_commit_date: 2022-01-12 04:46:27 -0500 (Wed, 12 Jan 2022)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  YES
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    ERROR    OK  
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    ERROR    OK  

Summary

Package: biomaRt
Version: 2.50.2
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:biomaRt.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings biomaRt_2.50.2.tar.gz
StartedAt: 2022-01-13 10:39:33 -0500 (Thu, 13 Jan 2022)
EndedAt: 2022-01-13 10:43:17 -0500 (Thu, 13 Jan 2022)
EllapsedTime: 224.1 seconds
RetCode: 1
Status:   ERROR  
CheckDir: biomaRt.Rcheck
Warnings: NA

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:biomaRt.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings biomaRt_2.50.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/biomaRt.Rcheck’
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘biomaRt/DESCRIPTION’ ... OK
* this is package ‘biomaRt’ version ‘2.50.2’
* 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 for sufficient/correct file permissions ... 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’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  > 
  > test_check("biomaRt", encoding = "UTF-8")
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test_listMarts.R:11:5): listMarts retruns a data.frame ───────────────
  Error: Unexpected format to the list of available marts.
  Please check the following URL manually, and try ?listMarts for advice.
  http://www.ensembl.org:80/biomart/martservice?type=registry&requestid=biomaRt
  Backtrace:
      █
   1. └─biomaRt::listMarts(host = "www.ensembl.org") test_listMarts.R:11:4
   2.   └─biomaRt:::.listMarts(...)
  
  [ FAIL 1 | WARN 3 | SKIP 0 | PASS 139 ]
  Error: Test failures
  Execution halted
* 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 ERROR, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.14-bioc/meat/biomaRt.Rcheck/00check.log’
for details.


Installation output

biomaRt.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL biomaRt
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘biomaRt’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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)

Tests output

biomaRt.Rcheck/tests/testthat.Rout.fail


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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")
══ Failed tests ════════════════════════════════════════════════════════════════
── Error (test_listMarts.R:11:5): listMarts retruns a data.frame ───────────────
Error: Unexpected format to the list of available marts.
Please check the following URL manually, and try ?listMarts for advice.
http://www.ensembl.org:80/biomart/martservice?type=registry&requestid=biomaRt
Backtrace:
    █
 1. └─biomaRt::listMarts(host = "www.ensembl.org") test_listMarts.R:11:4
 2.   └─biomaRt:::.listMarts(...)

[ FAIL 1 | WARN 3 | SKIP 0 | PASS 139 ]
Error: Test failures
Execution halted

Example timings

biomaRt.Rcheck/biomaRt-Ex.timings

nameusersystemelapsed
NP2009code000
attributePages000
exportFASTA0.0010.0000.001
filterType0.0000.0000.001
getBM0.0010.0000.001
getGene0.0010.0000.001
getLDS0.0010.0010.001
getSequence0.0010.0000.001
listAttributes0.0010.0000.001
listDatasets0.0010.0010.001
listEnsembl0.0000.0000.001
listEnsemblArchives0.2650.0290.739
listFilterValues0.0010.0010.001
listFilters0.0010.0000.001
listMarts000
select0.0010.0010.001
useDataset0.0000.0000.001
useEnsembl0.0000.0000.001
useMart000