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CHECK report for OmaDB on malbec1

This page was generated on 2020-04-15 12:13:33 -0400 (Wed, 15 Apr 2020).

Package 1175/1823HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
OmaDB 2.2.0
Klara Kaleb , Adrian Altenhoff
Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/OmaDB
Branch: RELEASE_3_10
Last Commit: 66d06e5
Last Changed Date: 2019-10-29 13:10:54 -0400 (Tue, 29 Oct 2019)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ WARNINGS ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: OmaDB
Version: 2.2.0
Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:OmaDB.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings OmaDB_2.2.0.tar.gz
StartedAt: 2020-04-15 05:19:32 -0400 (Wed, 15 Apr 2020)
EndedAt: 2020-04-15 05:24:35 -0400 (Wed, 15 Apr 2020)
EllapsedTime: 303.1 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: OmaDB.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:OmaDB.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings OmaDB_2.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/OmaDB.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘2.2.0’
* 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 or elapsed time > 5s
                 user system elapsed
getGenome      62.848  0.364  98.318
getGenomePairs 16.112  0.256  23.463
searchProtein   3.504  0.056   7.428
getOMAGroup     1.728  0.032   9.830
* 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
  ‘/home/biocbuild/bbs-3.10-bioc/meat/OmaDB.Rcheck/00check.log’
for details.



Installation output

OmaDB.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL OmaDB
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.10-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 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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
+ 
+ })
> 
> 
> 
> 
> proc.time()
   user  system elapsed 
  0.436   0.028   1.469 

Example timings

OmaDB.Rcheck/OmaDB-Ex.timings

nameusersystemelapsed
annotateSequence0.2480.0201.158
formatTopGO0.1560.0040.901
getAttribute0.4480.0001.996
getGenome62.848 0.36498.318
getGenomePairs16.112 0.25623.463
getHOG0.1520.0000.814
getLocus0.3280.0001.319
getOMAGroup1.7280.0329.830
getObjectAttributes0.2960.0001.245
getProtein0.2720.0121.231
getTaxonomy0.1080.0000.854
getTopGO1.2400.0483.827
getTree0.0160.0000.166
getVersion0.0160.0000.133
mapSequence0.7960.0244.334
resolveURL0.1240.0000.458
searchProtein3.5040.0567.428