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This page was generated on 2024-03-28 11:32:26 -0400 (Thu, 28 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson1macOS 13.6.1 Venturaarm644.3.3 (2024-02-29) -- "Angel Food Cake" 4376
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 1436/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
OGRE 1.6.0  (landing page)
Sven Berres
Snapshot Date: 2024-03-26 09:00:03 -0400 (Tue, 26 Mar 2024)
git_url: https://git.bioconductor.org/packages/OGRE
git_branch: RELEASE_3_18
git_last_commit: a47cbc3
git_last_commit_date: 2023-10-24 11:39:04 -0400 (Tue, 24 Oct 2023)
kjohnson1macOS 13.6.1 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published

CHECK results for OGRE on kjohnson1


To the developers/maintainers of the OGRE package:
- 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: 1.6.0
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_1.6.0.tar.gz
StartedAt: 2024-03-27 21:12:11 -0400 (Wed, 27 Mar 2024)
EndedAt: 2024-03-27 21:21:21 -0400 (Wed, 27 Mar 2024)
EllapsedTime: 550.7 seconds
RetCode: 0
Status:   OK  
CheckDir: OGRE.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### 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_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/OGRE.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘OGRE/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘OGRE’ version ‘1.6.0’
* 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 ... 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 32.869  0.658  37.634
covPlot           11.259  1.391  12.846
gvizPlot          10.593  0.300  19.631
* 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: OK


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/4.3-arm64/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 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (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... 
2024-03-27 21:21:07.065 R[8820:397909223] XType: Using static font registry.
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 9 ]
> 
> proc.time()
   user  system elapsed 
 69.735   1.954  83.235 

Example timings

OGRE.Rcheck/OGRE-Ex.timings

nameusersystemelapsed
OGREDataSet0.0090.0020.010
OGREDataSetFromDir0.0050.0020.007
addDataSetFromHub32.869 0.65837.634
addGRanges0.0730.0010.074
covPlot11.259 1.39112.846
extendGRanges0.8260.0550.882
extractPromoters0.4860.0810.567
fOverlaps0.6230.0140.638
gvizPlot10.593 0.30019.631
listPredefinedDataSets000
loadAnnotations0.2280.0050.236
makeExampleGRanges0.010.000.01
makeExampleOGREDataSet0.0040.0010.005
plotHist1.1200.0771.203
readDataSetFromFolder0.2340.0050.254
subsetGRanges0.3080.0050.313
sumPlot3.1630.0753.244
summarizeOverlap0.6070.0180.625