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This page was generated on 2025-12-10 07:00 -0500 (Wed, 10 Dec 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_64R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences" 4870
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 35/49HostnameOS / ArchINSTALLBUILDCHECK
MPO.db 0.99.8  (landing page)
Erqiang Hu
Snapshot Date: 2025-12-10 05:45 -0500 (Wed, 10 Dec 2025)
git_url: https://git.bioconductor.org/packages/MPO.db
git_branch: devel
git_last_commit: 653dfe0
git_last_commit_date: 2024-08-01 19:23:15 -0500 (Thu, 01 Aug 2024)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published


CHECK results for MPO.db on nebbiolo1

To the developers/maintainers of the MPO.db package:
- 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: MPO.db
Version: 0.99.8
Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:MPO.db.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings MPO.db_0.99.8.tar.gz
StartedAt: 2025-12-10 06:05:53 -0500 (Wed, 10 Dec 2025)
EndedAt: 2025-12-10 06:10:54 -0500 (Wed, 10 Dec 2025)
EllapsedTime: 301.4 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: MPO.db.Rcheck
Warnings: 1

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:MPO.db.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings MPO.db_0.99.8.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.23-data-annotation/meat/MPO.db.Rcheck’
* using R Under development (unstable) (2025-10-20 r88955)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘MPO.db/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MPO.db’ version ‘0.99.8’
* 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 ‘MPO.db’ 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 ... WARNING
Error while performing HEAD request.
   Proceeding without cache information.
MPO.db version 0.99.8

It looks like this package (or one of its dependent packages) has an
unstated dependence on a standard package.  All dependencies must be
declared in DESCRIPTION.
See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
* 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 ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING
See
  ‘/home/biocbuild/bbs-3.23-data-annotation/meat/MPO.db.Rcheck/00check.log’
for details.


Installation output

MPO.db.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL MPO.db
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’
* installing *source* package ‘MPO.db’ ...
** this is package ‘MPO.db’ version ‘0.99.8’
** 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 (MPO.db)

Tests output

MPO.db.Rcheck/tests/testthat.Rout


R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences"
Copyright (C) 2025 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)
> library(MPO.db)
MPO.db version 0.99.8
> test_check("MPO.db")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 13 ]
> 
> proc.time()
   user  system elapsed 
 13.755   2.648  16.859 

Example timings

MPO.db.Rcheck/MPO.db-Ex.timings

nameusersystemelapsed
MPOALIAS0.0110.0060.018
MPOANATOMY0.0460.0130.059
MPOANCESTOR0.1860.0230.210
MPOBASE0.0000.0010.000
MPOCHILDREN0.0430.0020.044
MPODb-class2.8730.5083.616
MPOMAPCOUNTS0.0630.0080.070
MPOMGIDO4.0450.4034.448
MPOMPDO0.0350.0020.037
MPOMPMGI0.5190.0410.559
MPOOFFSPRING0.1670.0050.171
MPOPARENTS0.0740.0160.090
MPOSYNONYM0.0780.0070.084
MPOTERM0.0640.0050.069
MPO_dbconn0.0000.0000.001
MPOmetadata0.1170.0090.127