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This page was generated on 2025-04-02 08:30 -0400 (Wed, 02 Apr 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2025-03-13 r87965) -- "Unsuffered Consequences" 4795
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 34/47HostnameOS / ArchINSTALLBUILDCHECK
MPO.db 0.99.8  (landing page)
Erqiang Hu
Snapshot Date: 2025-04-02 06:00 -0400 (Wed, 02 Apr 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 -0400 (Thu, 01 Aug 2024)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  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-3.21-bioc/R/bin/R CMD check --install=check:MPO.db.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings MPO.db_0.99.8.tar.gz
StartedAt: 2025-04-02 06:34:22 -0400 (Wed, 02 Apr 2025)
EndedAt: 2025-04-02 06:39:48 -0400 (Wed, 02 Apr 2025)
EllapsedTime: 325.8 seconds
RetCode: 0
Status:   OK  
CheckDir: MPO.db.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:MPO.db.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings MPO.db_0.99.8.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.21-data-annotation/meat/MPO.db.Rcheck’
* using R Under development (unstable) (2025-03-13 r87965)
* 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 24.04.2 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 ... 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 ... OK
* checking PDF version of manual ... OK
* DONE

Status: OK


Installation output

MPO.db.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL MPO.db
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.21-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) (2025-03-13 r87965) -- "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 
 10.578   1.373  12.465 

Example timings

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

nameusersystemelapsed
MPOALIAS0.0120.0020.014
MPOANATOMY0.0620.0080.070
MPOANCESTOR0.1340.0110.145
MPOBASE0.0010.0000.000
MPOCHILDREN0.0330.0010.035
MPODb-class2.2290.4352.898
MPOMAPCOUNTS0.0280.0000.029
MPOMGIDO2.7900.1832.974
MPOMPDO0.0310.0010.032
MPOMPMGI0.4350.0210.455
MPOOFFSPRING0.1500.0030.153
MPOPARENTS0.0540.0010.055
MPOSYNONYM0.0640.0010.064
MPOTERM0.0460.0000.047
MPO_dbconn000
MPOmetadata0.0680.0020.070