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This page was generated on 2024-02-22 12:48:11 -0500 (Thu, 22 Feb 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_64R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" 4657
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2024-01-14 r85805 ucrt) -- "Unsuffered Consequences" 4397
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 1104/2244HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
LRBaseDbi 2.13.0  (landing page)
Koki Tsuyuzaki
Snapshot Date: 2024-02-21 14:10:10 -0500 (Wed, 21 Feb 2024)
git_url: https://git.bioconductor.org/packages/LRBaseDbi
git_branch: devel
git_last_commit: 3a90c41
git_last_commit_date: 2023-10-24 11:06:45 -0500 (Tue, 24 Oct 2023)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    ERROR  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published

CHECK results for LRBaseDbi on nebbiolo1


To the developers/maintainers of the LRBaseDbi package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/LRBaseDbi.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: LRBaseDbi
Version: 2.13.0
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:LRBaseDbi.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings LRBaseDbi_2.13.0.tar.gz
StartedAt: 2024-02-22 00:09:57 -0500 (Thu, 22 Feb 2024)
EndedAt: 2024-02-22 00:11:36 -0500 (Thu, 22 Feb 2024)
EllapsedTime: 99.3 seconds
RetCode: 1
Status:   ERROR  
CheckDir: LRBaseDbi.Rcheck
Warnings: NA

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:LRBaseDbi.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings LRBaseDbi_2.13.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/LRBaseDbi.Rcheck’
* using R Under development (unstable) (2024-01-16 r85808)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.3 LTS
* using session charset: UTF-8
* checking for file ‘LRBaseDbi/DESCRIPTION’ ... OK
* this is package ‘LRBaseDbi’ version ‘2.13.0’
* 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 ‘LRBaseDbi’ 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 loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... 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 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 ... OK
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
  ...
--- re-building ‘LRBaseDbi.Rnw’ using Sweave
LRBase.XXX.eg.db-type packages are deprecated since Bioconductor 3.14. Use AnnotationHub instead. For details, check the vignette of LRBaseDbi

Error: processing vignette 'LRBaseDbi.Rnw' failed with diagnostics:
 chunk 2 
Error in library("AnnotationHub") : 
  there is no package called ‘AnnotationHub’

--- failed re-building ‘LRBaseDbi.Rnw’

SUMMARY: processing the following file failed:
  ‘LRBaseDbi.Rnw’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/LRBaseDbi.Rcheck/00check.log’
for details.


Installation output

LRBaseDbi.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL LRBaseDbi
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’
* installing *source* package ‘LRBaseDbi’ ...
** 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 (LRBaseDbi)

Tests output

LRBaseDbi.Rcheck/tests/testthat.Rout


R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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")
> 
> # Setting
> options(testthat.use_colours = FALSE)
> 
> test_file("testthat/test_methods.R")

══ Testing test_methods.R ══════════════════════════════════════════════════════

[ FAIL 0 | WARN 0 | SKIP 0 | PASS 0 ]
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ]

── Error ('test_methods.R:2:1'): (code run outside of `test_that()`) ───────────
<packageNotFoundError/error/condition>
Error in `library("AnnotationHub")`: there is no package called 'AnnotationHub'
Backtrace:
    ▆
 1. └─base::library("AnnotationHub") at test_methods.R:2:1

[ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ]
> 
> proc.time()
   user  system elapsed 
  4.271   0.227   4.489 

Example timings

LRBaseDbi.Rcheck/LRBaseDbi-Ex.timings

nameusersystemelapsed
LRBaseDb000