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This page was generated on 2024-03-18 11:38:00 -0400 (Mon, 18 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_64R Under development (unstable) (2024-03-06 r86056) -- "Unsuffered Consequences" 4685
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2024-03-06 r86056 ucrt) -- "Unsuffered Consequences" 4423
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-03-04 r86048) -- "Unsuffered Consequences" 4450
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-03-06 r86056) -- "Unsuffered Consequences" 4361
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 1422/2257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
OGRE 1.7.0  (landing page)
Sven Berres
Snapshot Date: 2024-03-17 14:00:14 -0400 (Sun, 17 Mar 2024)
git_url: https://git.bioconductor.org/packages/OGRE
git_branch: devel
git_last_commit: 323b550
git_last_commit_date: 2023-10-24 11:39:04 -0400 (Tue, 24 Oct 2023)
nebbiolo1Linux (Ubuntu 22.04.3 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
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  

CHECK results for OGRE on palomino3


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: 1.7.0
Command: F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:OGRE.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings OGRE_1.7.0.tar.gz
StartedAt: 2024-03-18 04:40:11 -0400 (Mon, 18 Mar 2024)
EndedAt: 2024-03-18 04:48:26 -0400 (Mon, 18 Mar 2024)
EllapsedTime: 494.6 seconds
RetCode: 0
Status:   OK  
CheckDir: OGRE.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:OGRE.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings OGRE_1.7.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/OGRE.Rcheck'
* using R Under development (unstable) (2024-03-06 r86056 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 12.3.0
    GNU Fortran (GCC) 12.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'OGRE/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'OGRE' version '1.7.0'
* 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 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 24.73   0.97   34.14
gvizPlot          10.48   0.43   14.66
covPlot            8.89   1.37   10.28
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'testthat.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... 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:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL OGRE
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.19-bioc/R/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 Under development (unstable) (2024-03-06 r86056 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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, 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 76 | SKIP 0 | PASS 9 ]

[ FAIL 0 | WARN 76 | SKIP 0 | PASS 9 ]
> 
> proc.time()
   user  system elapsed 
  57.03    3.34   64.00 

Example timings

OGRE.Rcheck/OGRE-Ex.timings

nameusersystemelapsed
OGREDataSet000
OGREDataSetFromDir0.000.000.01
addDataSetFromHub24.73 0.9734.14
addGRanges0.110.000.11
covPlot 8.89 1.3710.28
extendGRanges0.880.131.00
extractPromoters0.610.040.66
fOverlaps0.890.141.03
gvizPlot10.48 0.4314.66
listPredefinedDataSets000
loadAnnotations0.220.000.22
makeExampleGRanges000
makeExampleOGREDataSet0.000.010.01
plotHist1.200.031.24
readDataSetFromFolder0.270.000.26
subsetGRanges0.420.020.44
sumPlot2.190.112.42
summarizeOverlap0.720.000.72