Back to Multiple platform build/check report for BioC 3.20:   simplified   long
A[B]CDEFGHIJKLMNOPQRSTUVWXYZ

This page was generated on 2024-06-11 15:40 -0400 (Tue, 11 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" 4679
palomino4Windows Server 2022 Datacenterx644.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" 4414
merida1macOS 12.7.4 Montereyx86_644.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 4441
kjohnson1macOS 13.6.6 Venturaarm644.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 4394
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

Package 205/2239HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
biomaRt 2.61.0  (landing page)
Mike Smith
Snapshot Date: 2024-06-09 14:00 -0400 (Sun, 09 Jun 2024)
git_url: https://git.bioconductor.org/packages/biomaRt
git_branch: devel
git_last_commit: 5efb280
git_last_commit_date: 2024-04-30 10:13:37 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    ERROR  
palomino4Windows Server 2022 Datacenter / x64  OK    OK    ERROR    OK  
merida1macOS 12.7.4 Monterey / x86_64  OK    OK    ERROR    OK  
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    ERROR    OK  


CHECK results for biomaRt on palomino4

To the developers/maintainers of the biomaRt package:
- 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 Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: biomaRt
Version: 2.61.0
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:biomaRt.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings biomaRt_2.61.0.tar.gz
StartedAt: 2024-06-10 00:21:30 -0400 (Mon, 10 Jun 2024)
EndedAt: 2024-06-10 00:24:22 -0400 (Mon, 10 Jun 2024)
EllapsedTime: 172.1 seconds
RetCode: 1
Status:   ERROR  
CheckDir: biomaRt.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:biomaRt.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings biomaRt_2.61.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/biomaRt.Rcheck'
* using R version 4.4.0 RC (2024-04-16 r86468 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'biomaRt/DESCRIPTION' ... OK
* this is package 'biomaRt' version '2.61.0'
* 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 code 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:
  > library(testthat)
  > library(mockery)
  > library(biomaRt)
  > library(httptest2)
  > 
  > test_check("biomaRt", encoding = "UTF-8")
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 155 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test_ensembl_ssl_settings.R:64:5'): SSL settings are stored in the cache ──
  `http_config <- .getEnsemblSSL()` produced messages.
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 155 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... 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
  'F:/biocbuild/bbs-3.20-bioc/meat/biomaRt.Rcheck/00check.log'
for details.


Installation output

biomaRt.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL biomaRt
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.20-bioc/R/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 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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)
> library(httptest2)
> 
> test_check("biomaRt", encoding = "UTF-8")
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 155 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test_ensembl_ssl_settings.R:64:5'): SSL settings are stored in the cache ──
`http_config <- .getEnsemblSSL()` produced messages.

[ FAIL 1 | WARN 0 | SKIP 0 | PASS 155 ]
Error: Test failures
Execution halted

Example timings

biomaRt.Rcheck/biomaRt-Ex.timings

nameusersystemelapsed
NP2009code000
attributePages000
exportFASTA000
filterType000
getBM000
getGene0.010.000.02
getLDS000
getSequence000
listAttributes000
listDatasets000
listEnsembl000
listEnsemblArchives0.550.140.72
listFilterValues000
listFilters0.020.000.01
listMarts000
select000
setEnsemblSSL000
useDataset000
useEnsembl000
useMart000