Package: roma

Version: 0.99.11

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:roma.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings roma_0.99.11.tar.gz

StartedAt: 2018-04-26 01:54:28 -0400 (Thu, 26 Apr 2018)

EndedAt: 2018-04-26 01:58:56 -0400 (Thu, 26 Apr 2018)

EllapsedTime: 267.8 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: roma.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:roma.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings roma_0.99.11.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/roma.Rcheck’
* using R version 3.5.0 RC (2018-04-15 r74605)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘roma/DESCRIPTION’ ... OK
* this is package ‘roma’ version ‘0.99.11’
* 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 ‘roma’ 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
Namespace in Imports field not imported from: ‘ape’
  All declared Imports should be used.
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 ... WARNING
Undocumented code objects:
  ‘group’ ‘hog’ ‘orthologs’ ‘pairs’ ‘protein’ ‘seq_protein’
  ‘sequence_annotation’ ‘sequence_map’ ‘taxonomy’ ‘xref’
Undocumented data sets:
  ‘group’ ‘hog’ ‘orthologs’ ‘pairs’ ‘protein’ ‘seq_protein’
  ‘sequence_annotation’ ‘sequence_map’ ‘taxonomy’ ‘xref’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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
getXref       4.136  0.094   7.061
getTopGO      0.978  0.069   5.075
mapSequence   0.643  0.091  31.053
getOntologies 0.503  0.074   6.086
resolveURL    0.151  0.014  60.904
* 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, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.8-bioc/meat/roma.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 roma
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘roma’ ...
** 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 (roma)

R version 3.5.0 RC (2018-04-15 r74605) -- "Joy in Playing"
Copyright (C) 2018 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)
> library(roma)
Loading required package: httr
Loading required package: plyr

> 
> 
> test_that("Testing the correct format returned", {
+     expect_equal(class(getData("group","YEAST58")$members), "data.frame")
+     expect_equal(class(getXref(pattern="MAL")), "data.frame")
+     expect_equal(class(getData("genome","YEAST")), "list")
+     expect_equal(class(getGenomeAlignment("ASHGO","YEAST")), "data.frame")
+ 
+ 	})
>  	
> 
> 	
> test_that("Testing the URL validity", {
+   expect_equal(status_code(httr::GET("https://omabrowser.org/api")), 200 ) #checking that the server is live and accesible
+ 
+ })
> 
> 
> 
> 
> proc.time()
   user  system elapsed 
 10.285   0.493  16.668 

name	user	system	elapsed
childrenMembers	0.293	0.020	0.941
formatTopGO	0.155	0.017	4.334
getAnnotation	0.071	0.007	4.143
getAttribute	0.021	0.003	0.309
getData	0.045	0.009	0.284
getGRanges	0.041	0.006	0.310
getGenomeAlignment	0.960	0.041	3.335
getHOG	0.040	0.010	0.392
getObjectAttributes	0.033	0.005	0.305
getOntologies	0.503	0.074	6.086
getSequences	0.220	0.039	1.536
getTaxonomy	0.158	0.016	1.199
getTopGO	0.978	0.069	5.075
getXref	4.136	0.094	7.061
mapSequence	0.643	0.091	31.053
resolveURL	0.151	0.014	60.904