Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-05-20 12:05:40 -0400 (Fri, 20 May 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4380
palomino3Windows Server 2022 Datacenterx644.2.0 (2022-04-22 ucrt) -- "Vigorous Calisthenics" 4155
merida1macOS 10.14.6 Mojavex86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4221
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

CHECK results for OmaDB on nebbiolo1


To the developers/maintainers of the OmaDB package:
- Please 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 How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1356/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
OmaDB 2.12.0  (landing page)
Klara Kaleb , Adrian Altenhoff
Snapshot Date: 2022-05-19 13:55:15 -0400 (Thu, 19 May 2022)
git_url: https://git.bioconductor.org/packages/OmaDB
git_branch: RELEASE_3_15
git_last_commit: 1c7747a
git_last_commit_date: 2022-04-26 11:45:37 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: OmaDB
Version: 2.12.0
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:OmaDB.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings OmaDB_2.12.0.tar.gz
StartedAt: 2022-05-19 20:40:14 -0400 (Thu, 19 May 2022)
EndedAt: 2022-05-19 20:50:49 -0400 (Thu, 19 May 2022)
EllapsedTime: 635.3 seconds
RetCode: 0
Status:   OK  
CheckDir: OmaDB.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:OmaDB.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings OmaDB_2.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/OmaDB.Rcheck’
* using R version 4.2.0 (2022-04-22)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘OmaDB/DESCRIPTION’ ... OK
* this is package ‘OmaDB’ version ‘2.12.0’
* 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 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 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 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           152.406  2.556 261.533
getGenomePairs       13.737  1.621  34.118
getOMAGroup           2.456  0.372   9.327
mapSequence           2.570  0.208   9.896
getObjectAttributes   1.022  0.028   5.434
searchProtein         0.052  0.005 187.315
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: OK


Installation output

OmaDB.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL OmaDB
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.15-bioc/R/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 4.2.0 (2022-04-22) -- "Vigorous Calisthenics"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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 
  0.842   0.045   2.286 

Example timings

OmaDB.Rcheck/OmaDB-Ex.timings

nameusersystemelapsed
annotateSequence0.1010.0202.448
formatTopGO0.1020.0040.578
getAttribute0.4920.0723.594
getGenome152.406 2.556261.533
getGenomePairs13.737 1.62134.118
getHOG0.1560.0230.756
getLocus0.5980.0362.940
getOMAGroup2.4560.3729.327
getObjectAttributes1.0220.0285.434
getProtein0.3360.0241.749
getTaxonomy0.0800.0040.985
getTopGO1.7430.1683.839
getTree0.0130.0080.173
getVersion0.0180.0000.172
mapSequence2.5700.2089.896
resolveURL0.0930.0040.551
searchProtein 0.052 0.005187.315