Back to Multiple platform build/check report for BioC 3.13
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This page was generated on 2021-09-20 15:04:55 -0400 (Mon, 20 Sep 2021).

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? here 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 1295/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
OmaDB 2.8.0  (landing page)
Klara Kaleb , Adrian Altenhoff
Snapshot Date: 2021-09-19 04:50:10 -0400 (Sun, 19 Sep 2021)
git_url: https://git.bioconductor.org/packages/OmaDB
git_branch: RELEASE_3_13
git_last_commit: 73c1e16
git_last_commit_date: 2021-05-19 12:32:07 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: OmaDB
Version: 2.8.0
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:OmaDB.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings OmaDB_2.8.0.tar.gz
StartedAt: 2021-09-19 10:48:42 -0400 (Sun, 19 Sep 2021)
EndedAt: 2021-09-19 11:00:13 -0400 (Sun, 19 Sep 2021)
EllapsedTime: 691.6 seconds
RetCode: 0
Status:   OK  
CheckDir: OmaDB.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:OmaDB.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings OmaDB_2.8.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/OmaDB.Rcheck’
* using R version 4.1.1 (2021-08-10)
* 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 ‘2.8.0’
* 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      177.717  2.860 303.165
getGenomePairs  22.719  1.841  55.486
getOMAGroup      3.042  0.354  10.270
mapSequence      2.614  0.171   7.362
searchProtein    0.037  0.005 187.297
* 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-3.13-bioc/R/bin/R CMD INSTALL OmaDB
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.13-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 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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 
  0.720   0.083   2.173 

Example timings

OmaDB.Rcheck/OmaDB-Ex.timings

nameusersystemelapsed
annotateSequence0.1990.0083.934
formatTopGO0.5960.0081.068
getAttribute0.2850.0561.825
getGenome177.717 2.860303.165
getGenomePairs22.719 1.84155.486
getHOG0.2000.0070.946
getLocus0.4650.0241.659
getOMAGroup 3.042 0.35410.270
getObjectAttributes0.4870.0001.812
getProtein0.4250.0361.318
getTaxonomy0.0900.0041.194
getTopGO1.8730.1124.447
getTree0.0250.0000.163
getVersion0.0210.0000.120
mapSequence2.6140.1717.362
resolveURL0.0570.0010.362
searchProtein 0.037 0.005187.297