Package: OmaDB

Version: 1.0.1

Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:OmaDB.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings OmaDB_1.0.1.tar.gz

StartedAt: 2018-10-16 02:25:34 -0400 (Tue, 16 Oct 2018)

EndedAt: 2018-10-16 02:29:23 -0400 (Tue, 16 Oct 2018)

EllapsedTime: 228.5 seconds

RetCode: 0

Status:  OK

CheckDir: OmaDB.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:OmaDB.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings OmaDB_1.0.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/OmaDB.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* 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 ‘1.0.1’
* 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 ... NOTE
Missing or unexported object: ‘topGO::annFUN.GO2gene’
* 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
getOntologies 8.716  0.056  58.614
getSequences  4.572  0.048  30.968
getXref       2.448  0.028   6.969
mapSequence   0.424  0.004  11.128
resolveURL    0.368  0.004   9.463
* 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 NOTE
See
  ‘/home/biocbuild/bbs-3.7-bioc/meat/OmaDB.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL OmaDB
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/library’
* installing *source* package ‘OmaDB’ ...
** R
** data
*** moving datasets to lazyload DB
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (OmaDB)

R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
Copyright (C) 2018 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 
  0.412   0.052   3.181 

name	user	system	elapsed
formatTopGO	1.520	0.032	2.680
getAnnotation	0.048	0.000	0.462
getAttribute	0.532	0.000	1.589
getData	0.036	0.004	0.292
getGRanges	0.280	0.012	1.340
getGenomeAlignment	0.820	0.040	2.754
getHOG	0.124	0.004	0.522
getObjectAttributes	0.212	0.004	1.252
getOntologies	8.716	0.056	58.614
getSequences	4.572	0.048	30.968
getTaxonomy	0.080	0.000	1.646
getTopGO	0.700	0.024	1.292
getXref	2.448	0.028	6.969
mapSequence	0.424	0.004	11.128
resolveURL	0.368	0.004	9.463