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CHECK report for OmaDB on malbec2

This page was generated on 2018-10-17 08:31:01 -0400 (Wed, 17 Oct 2018).

Package 1016/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
OmaDB 1.0.1
Klara Kaleb , Adrian Altenhoff
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/OmaDB
Branch: RELEASE_3_7
Last Commit: e902bdf
Last Changed Date: 2018-06-29 07:06:48 -0400 (Fri, 29 Jun 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

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

Command output

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###
### 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
###
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* 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.



Installation output

OmaDB.Rcheck/00install.out

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###
### 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)

Tests output

OmaDB.Rcheck/tests/testthat.Rout


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 

Example timings

OmaDB.Rcheck/OmaDB-Ex.timings

nameusersystemelapsed
formatTopGO1.5200.0322.680
getAnnotation0.0480.0000.462
getAttribute0.5320.0001.589
getData0.0360.0040.292
getGRanges0.2800.0121.340
getGenomeAlignment0.8200.0402.754
getHOG0.1240.0040.522
getObjectAttributes0.2120.0041.252
getOntologies 8.716 0.05658.614
getSequences 4.572 0.04830.968
getTaxonomy0.0800.0001.646
getTopGO0.7000.0241.292
getXref2.4480.0286.969
mapSequence 0.424 0.00411.128
resolveURL0.3680.0049.463