Package: OmaDB

Version: 2.3.0

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_2.3.0.tar.gz

StartedAt: 2020-01-16 07:04:11 -0500 (Thu, 16 Jan 2020)

EndedAt: 2020-01-16 07:10:41 -0500 (Thu, 16 Jan 2020)

EllapsedTime: 390.0 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: OmaDB.Rcheck

Warnings: 1

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### Running command:
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###   /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_2.3.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/OmaDB.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘OmaDB/DESCRIPTION’ ... OK
* this is package ‘OmaDB’ version ‘2.3.0’
* 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 (user + system) or elapsed time > 5s
                 user system elapsed
getGenome      91.195  2.013 114.778
getGenomePairs 27.930  1.208  35.763
searchProtein   6.521  0.342  10.227
getOMAGroup     2.630  0.126   7.489
mapSequence     2.087  0.064   7.250
* 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-3.11-bioc/meat/OmaDB.Rcheck/00check.log’
for details.

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

R Under development (unstable) (2019-12-14 r77572) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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
+ 
+ })
> 
> 
> 
> 
> proc.time()
   user  system elapsed 
  0.608   0.219   1.980 

name	user	system	elapsed
annotateSequence	0.320	0.039	1.217
formatTopGO	0.342	0.003	2.430
getAttribute	0.077	0.000	0.373
getGenome	91.195	2.013	114.778
getGenomePairs	27.930	1.208	35.763
getHOG	0.118	0.005	0.757
getLocus	0.148	0.000	0.424
getOMAGroup	2.630	0.126	7.489
getObjectAttributes	0.108	0.001	0.393
getProtein	0.387	0.010	2.966
getTaxonomy	0.143	0.006	0.970
getTopGO	2.146	0.134	2.870
getTree	0.018	0.001	0.175
getVersion	0.014	0.001	0.130
mapSequence	2.087	0.064	7.250
resolveURL	0.099	0.006	0.445
searchProtein	6.521	0.342	10.227