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This page was generated on 2023-10-14 11:35:32 -0400 (Sat, 14 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.2 LTS)x86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4626
palomino3Windows Server 2022 Datacenterx644.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" 4379
merida1macOS 12.6.4 Montereyx86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4395
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

Package 1409/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
OGRE 1.4.0  (landing page)
Sven Berres
Snapshot Date: 2023-10-13 14:00:12 -0400 (Fri, 13 Oct 2023)
git_url: https://git.bioconductor.org/packages/OGRE
git_branch: RELEASE_3_17
git_last_commit: 4f0404e
git_last_commit_date: 2023-04-25 11:35:27 -0400 (Tue, 25 Apr 2023)
nebbiolo1Linux (Ubuntu 22.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.6.4 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson2macOS 12.6.1 Monterey / arm64see weekly results here

CHECK results for OGRE on nebbiolo1


To the developers/maintainers of the OGRE package:
- 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 Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: OGRE
Version: 1.4.0
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:OGRE.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings OGRE_1.4.0.tar.gz
StartedAt: 2023-10-13 23:27:00 -0400 (Fri, 13 Oct 2023)
EndedAt: 2023-10-13 23:36:29 -0400 (Fri, 13 Oct 2023)
EllapsedTime: 568.3 seconds
RetCode: 0
Status:   OK  
CheckDir: OGRE.Rcheck
Warnings: 0

Command output

##############################################################################
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### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:OGRE.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings OGRE_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/OGRE.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
* running under: Ubuntu 22.04.3 LTS
* using session charset: UTF-8
* checking for file ‘OGRE/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘OGRE’ version ‘1.4.0’
* 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 loading without being on the library search path ... 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
addDataSetFromHub 24.991  2.471  28.480
gvizPlot          15.595  1.308  26.584
covPlot           12.393  0.599  10.855
sumPlot            4.214  0.099   5.286
* 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 ...
  ‘OGRE.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: OK


Installation output

OGRE.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL OGRE
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-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 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 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)
> 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, aperm, 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 object is masked from 'package:utils':

    findMatches

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... 
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 0 | SKIP 0 | PASS 9 ]
> 
> proc.time()
   user  system elapsed 
 75.385   4.162  91.378 

Example timings

OGRE.Rcheck/OGRE-Ex.timings

nameusersystemelapsed
OGREDataSet0.0090.0000.010
OGREDataSetFromDir0.0050.0000.004
addDataSetFromHub24.991 2.47128.480
addGRanges0.1680.0000.168
covPlot12.393 0.59910.855
extendGRanges0.7650.0240.788
extractPromoters0.3590.0080.366
fOverlaps0.5910.0040.578
gvizPlot15.595 1.30826.584
listPredefinedDataSets000
loadAnnotations0.3160.0040.362
makeExampleGRanges0.0200.0070.027
makeExampleOGREDataSet0.0060.0000.007
plotHist1.9560.0562.356
readDataSetFromFolder0.4080.0000.412
subsetGRanges0.6610.0230.685
sumPlot4.2140.0995.286
summarizeOverlap1.5250.0551.565