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CHECK report for OmaDB on merida1

This page was generated on 2021-05-06 12:36:00 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the OmaDB package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1250/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
OmaDB 2.6.1  (landing page)
Klara Kaleb , Adrian Altenhoff
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/OmaDB
Branch: RELEASE_3_12
Last Commit: f70bed3
Last Changed Date: 2020-11-10 17:30:16 -0400 (Tue, 10 Nov 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version exists in internal repository

Summary

Package: OmaDB
Version: 2.6.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:OmaDB.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings OmaDB_2.6.1.tar.gz
StartedAt: 2021-05-06 04:20:11 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 04:29:17 -0400 (Thu, 06 May 2021)
EllapsedTime: 545.6 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: OmaDB.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:OmaDB.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings OmaDB_2.6.1.tar.gz
###
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##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/OmaDB.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘OmaDB/DESCRIPTION’ ... OK
* this is package ‘OmaDB’ version ‘2.6.1’
* 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 ... WARNING
  install.R
These files are defunct. See manual ‘Writing R Extensions’.
* 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 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      99.491  1.756 136.956
getGenomePairs 31.920  1.070  40.967
getOMAGroup     2.670  0.106   8.133
mapSequence     1.399  0.085   5.089
searchProtein   0.030  0.006 187.627
* 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: 1 WARNING
See
  ‘/Users/biocbuild/bbs-3.12-bioc/meat/OmaDB.Rcheck/00check.log’
for details.



Installation output

OmaDB.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL OmaDB
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/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 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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 
  1.490   0.131   2.938 

Example timings

OmaDB.Rcheck/OmaDB-Ex.timings

nameusersystemelapsed
annotateSequence0.2820.0201.260
formatTopGO0.1930.0010.768
getAttribute0.7310.0031.785
getGenome 99.491 1.756136.956
getGenomePairs31.920 1.07040.967
getHOG0.1710.0071.235
getLocus0.4980.0021.498
getOMAGroup2.6700.1068.133
getObjectAttributes0.3990.0031.376
getProtein0.2400.0061.241
getTaxonomy0.1450.0031.049
getTopGO1.1200.0281.706
getTree0.0090.0010.180
getVersion0.0080.0010.135
mapSequence1.3990.0855.089
resolveURL0.0670.0030.420
searchProtein 0.030 0.006187.627