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This page was generated on 2024-12-23 12:04 -0500 (Mon, 23 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4744
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4487
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4515
kjohnson1macOS 13.6.6 Venturaarm644.4.2 (2024-10-31) -- "Pile of Leaves" 4467
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 1446/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
OmaDB 2.22.0  (landing page)
Klara Kaleb , Adrian Altenhoff
Snapshot Date: 2024-12-19 13:00 -0500 (Thu, 19 Dec 2024)
git_url: https://git.bioconductor.org/packages/OmaDB
git_branch: RELEASE_3_20
git_last_commit: e74de93
git_last_commit_date: 2024-10-29 10:24:16 -0500 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for OmaDB on nebbiolo2

To the developers/maintainers of the OmaDB package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/OmaDB.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: OmaDB
Version: 2.22.0
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:OmaDB.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings OmaDB_2.22.0.tar.gz
StartedAt: 2024-12-20 03:48:16 -0500 (Fri, 20 Dec 2024)
EndedAt: 2024-12-20 03:56:54 -0500 (Fri, 20 Dec 2024)
EllapsedTime: 518.5 seconds
RetCode: 0
Status:   OK  
CheckDir: OmaDB.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:OmaDB.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings OmaDB_2.22.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/OmaDB.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘OmaDB/DESCRIPTION’ ... OK
* this is package ‘OmaDB’ version ‘2.22.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘OmaDB’ 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 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 ... NOTE
Documented arguments not in \usage in Rd file 'getGenomeAlignment-deprecated.Rd':
  ‘genome_id1’ ‘genome_id2’ ‘per_page’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
getGenome      143.897  1.295 224.874
getGenomePairs  14.872  0.486  21.270
getOMAGroup      1.609  0.026   9.550
mapSequence      0.861  0.007   6.398
getProtein       0.210  0.003   5.467
* 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 NOTE
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/OmaDB.Rcheck/00check.log’
for details.


Installation output

OmaDB.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL OmaDB
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘OmaDB’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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 (OmaDB)

Tests output

OmaDB.Rcheck/tests/testthat.Rout


R version 4.4.2 (2024-10-31) -- "Pile of Leaves"
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)
> 
> test_that("Testing the URL validity", {
+   expect_equal(httr::status_code(httr::GET("https://omabrowser.org/api")), 200 ) #checking that the server is live and accesible
+ 
+ })
Test passed 🎊
> 
> 
> 
> 
> proc.time()
   user  system elapsed 
  0.912   0.061   2.626 

Example timings

OmaDB.Rcheck/OmaDB-Ex.timings

nameusersystemelapsed
annotateSequence0.6840.2042.085
formatTopGO0.1090.0252.530
getAttribute0.0160.0000.134
getGenome143.897 1.295224.874
getGenomePairs14.872 0.48621.270
getHOG0.0770.0090.475
getLocus0.0470.0030.171
getOMAGroup1.6090.0269.550
getObjectAttributes0.0130.0010.123
getProtein0.2100.0035.467
getTaxonomy0.0650.0010.696
getTopGO0.8980.0471.480
getTree0.0110.0010.164
getVersion0.1090.0200.214
mapSequence0.8610.0076.398
resolveURL0.0280.0002.473
searchProtein0.0120.0013.908