Back to Multiple platform build/check report for BioC 3.15
ABCDEFGHIJKLMN[O]PQRSTUVWXYZ

This page was generated on 2022-08-08 13:20:37 -0400 (Mon, 08 Aug 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4362
merida1macOS 10.14.6 Mojavex86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4180
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for OGRE on merida1


To the developers/maintainers of the OGRE package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/OGRE.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1351/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
OGRE 1.0.0  (landing page)
Sven Berres
Snapshot Date: 2022-08-07 13:55:12 -0400 (Sun, 07 Aug 2022)
git_url: https://git.bioconductor.org/packages/OGRE
git_branch: RELEASE_3_15
git_last_commit: 5f9a0d1
git_last_commit_date: 2022-04-26 12:20:43 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: OGRE
Version: 1.0.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:OGRE.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings OGRE_1.0.0.tar.gz
StartedAt: 2022-08-08 05:33:48 -0400 (Mon, 08 Aug 2022)
EndedAt: 2022-08-08 05:45:56 -0400 (Mon, 08 Aug 2022)
EllapsedTime: 728.0 seconds
RetCode: 0
Status:   OK  
CheckDir: OGRE.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:OGRE.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings OGRE_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/OGRE.Rcheck’
* using R version 4.2.1 (2022-06-23)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘OGRE/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘OGRE’ version ‘1.0.0’
* package encoding: UTF-8
* 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 ‘OGRE’ 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
addDataSetFromHub: no visible binding for global variable 'name'
addDataSetFromHub: no visible binding for global variable 'ID'
covPlot: no visible binding for global variable 'subjType'
covPlot : <anonymous>: no visible binding for global variable 'queryID'
covPlot : <anonymous>: no visible binding for global variable
  'subjType'
covPlot : <anonymous>: no visible binding for global variable 'bins'
covPlot : <anonymous>: no visible binding for global variable 'rCov'
covPlot: no visible binding for global variable 'ID'
covPlot: no visible binding for global variable 'x'
covPlot: no visible binding for global variable 'Coverage'
sumPlot: no visible binding for global variable 'queryLog'
Undefined global functions or variables:
  Coverage ID bins name queryID queryLog rCov subjType x
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
addDataSetFromHub 37.093  1.145  46.492
covPlot           14.531  1.332  15.901
gvizPlot          12.582  0.165  15.304
* 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
  ‘/Users/biocbuild/bbs-3.15-bioc/meat/OGRE.Rcheck/00check.log’
for details.



Installation output

OGRE.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL OGRE
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library’
* installing *source* package ‘OGRE’ ...
** using staged installation
** R
** 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 (OGRE)

Tests output

OGRE.Rcheck/tests/testthat.Rout


R version 4.2.1 (2022-06-23) -- "Funny-Looking Kid"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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(OGRE)
Loading required package: S4Vectors
Loading required package: stats4
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min


Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    I, expand.grid, unname

> 
> test_check("OGRE")
Initializing OGREDataSet... 
Initializing OGREDataSet... 
Initializing OGREDataSet... 
Reading query dataset... 
Reading subject datasets... 
snapshotDate(): 2022-04-25
loading from cache
require("GenomicRanges")
Added protCodingGenes
Initializing OGREDataSet... 
Reading query dataset... 
Reading subject datasets... 
Initializing OGREDataSet... 
Reading query dataset... 
Reading subject datasets... 
Initializing OGREDataSet... 
Reading query dataset... 
Reading subject datasets... 
Plotting query: ENSG00000142168
Initializing OGREDataSet... 
Reading query dataset... 
Reading subject datasets... 
Initializing OGREDataSet... 
Reading query dataset... 
Reading subject datasets... 
[ FAIL 0 | WARN 3 | SKIP 0 | PASS 9 ]

[ FAIL 0 | WARN 3 | SKIP 0 | PASS 9 ]
> 
> proc.time()
   user  system elapsed 
 90.798   2.686 102.194 

Example timings

OGRE.Rcheck/OGRE-Ex.timings

nameusersystemelapsed
OGREDataSet0.0170.0010.018
OGREDataSetFromDir0.0080.0010.009
addDataSetFromHub37.093 1.14546.492
addGRanges0.1680.0010.170
covPlot14.531 1.33215.901
extendGRanges1.7320.1011.853
extractPromoters0.8580.0810.944
fOverlaps1.4020.1331.548
gvizPlot12.582 0.16515.304
listPredefinedDataSets0.0000.0000.001
loadAnnotations0.4500.0040.455
makeExampleGRanges0.0210.0010.022
makeExampleOGREDataSet0.0060.0000.006
plotHist1.9410.0301.981
readDataSetFromFolder0.5060.0390.547
subsetGRanges0.6150.0030.623
sumPlot4.4130.0594.521
summarizeOverlap1.2940.0061.304