Sven Berres
| Snapshot Date: 2022-03-16 13:55:23 -0400 (Wed, 16 Mar 2022) |
| git_url: https://git.bioconductor.org/packages/OGRE |
| git_branch: master |
| git_last_commit: 867a785 |
| git_last_commit_date: 2022-03-08 05:34:17 -0400 (Tue, 08 Mar 2022) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-03-17 11:08:24 -0400 (Thu, 17 Mar 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" | 4334 |
| riesling1 | Windows Server 2019 Standard | x64 | R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" | 4060 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" | 4083 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" | 4134 |
| 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 | ||||
|
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? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1324/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| OGRE 0.99.8 (landing page) Sven Berres
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| riesling1 | Windows Server 2019 Standard / x64 | OK | OK | WARNINGS | OK | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | ERROR | OK | |||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | ERROR | skipped | skipped | |||||||||
| Package: OGRE |
| Version: 0.99.8 |
| Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:OGRE.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings OGRE_0.99.8.tar.gz |
| StartedAt: 2022-03-16 19:43:18 -0400 (Wed, 16 Mar 2022) |
| EndedAt: 2022-03-16 19:49:55 -0400 (Wed, 16 Mar 2022) |
| EllapsedTime: 396.4 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: OGRE.Rcheck |
| Warnings: 1 |
##############################################################################
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:OGRE.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings OGRE_0.99.8.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/OGRE.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'OGRE/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'OGRE' version '0.99.8'
* 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 ... WARNING
Found the following significant warnings:
Warning: replacing previous import 'GenomicRanges::shift' by 'data.table::shift' when loading 'OGRE'
Warning: replacing previous import 'S4Vectors::second' by 'data.table::second' when loading 'OGRE'
Warning: replacing previous import 'S4Vectors::first' by 'data.table::first' when loading 'OGRE'
See 'D:/biocbuild/bbs-3.15-bioc/meat/OGRE.Rcheck/00install.out' for details.
* 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
SHREC : <anonymous>: no visible binding for global variable 'queryID'
addDataSetFromHub: no visible binding for global variable 'name'
addDataSetFromHub: no visible binding for global variable 'ID'
sumPlot: no visible binding for global variable 'queryLog'
Undefined global functions or variables:
ID name queryID queryLog
* 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 24.75 1.44 30.39
gvizPlot 7.62 0.30 12.60
sumPlot 2.87 0.18 5.49
* 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
'D:/biocbuild/bbs-3.15-bioc/meat/OGRE.Rcheck/00check.log'
for details.
OGRE.Rcheck/00install.out
##############################################################################
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL OGRE
###
##############################################################################
##############################################################################
* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'OGRE' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import 'GenomicRanges::shift' by 'data.table::shift' when loading 'OGRE'
Warning: replacing previous import 'S4Vectors::second' by 'data.table::second' when loading 'OGRE'
Warning: replacing previous import 'S4Vectors::first' by 'data.table::first' when loading 'OGRE'
** help
*** installing help indices
converting help for package 'OGRE'
finding HTML links ... done
OGRE-package html
OGREDataSet html
OGREDataSetFromDir html
SHREC html
addDataSetFromHub html
addGRanges html
extendGRanges html
extractPromoters html
fOverlaps html
gvizPlot html
listPredefinedDataSets html
loadAnnotations html
makeExampleGRanges html
makeExampleOGREDataSet html
plotHist html
readDataSetFromFolder html
readQuery html
readSubject html
subsetGRanges html
sumPlot html
summarizeOverlap html
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import 'GenomicRanges::shift' by 'data.table::shift' when loading 'OGRE'
Warning: replacing previous import 'S4Vectors::second' by 'data.table::second' when loading 'OGRE'
Warning: replacing previous import 'S4Vectors::first' by 'data.table::first' when loading 'OGRE'
** testing if installed package can be loaded from final location
Warning: replacing previous import 'GenomicRanges::shift' by 'data.table::shift' when loading 'OGRE'
Warning: replacing previous import 'S4Vectors::second' by 'data.table::second' when loading 'OGRE'
Warning: replacing previous import 'S4Vectors::first' by 'data.table::first' when loading 'OGRE'
** testing if installed package keeps a record of temporary installation path
* DONE (OGRE)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
DESCRIPTION file of package 'primirTSS' is missing or broken
done
OGRE.Rcheck/tests/testthat.Rout
R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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
Warning messages:
1: replacing previous import 'GenomicRanges::shift' by 'data.table::shift' when loading 'OGRE'
2: replacing previous import 'S4Vectors::second' by 'data.table::second' when loading 'OGRE'
3: replacing previous import 'S4Vectors::first' by 'data.table::first' when loading 'OGRE'
>
> test_check("OGRE")
Initializing OGREDataSet...
Initializing OGREDataSet...
Initializing OGREDataSet...
Reading query dataset...
Reading subject datasets...
snapshotDate(): 2022-02-22
loading from cache
require("GenomicRanges")
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
47.96 3.40 64.00
OGRE.Rcheck/OGRE-Ex.timings
| name | user | system | elapsed | |
| OGREDataSet | 0.01 | 0.00 | 0.02 | |
| OGREDataSetFromDir | 0.02 | 0.00 | 0.01 | |
| addDataSetFromHub | 24.75 | 1.44 | 30.39 | |
| addGRanges | 0.11 | 0.00 | 0.25 | |
| extendGRanges | 2.25 | 0.19 | 2.82 | |
| extractPromoters | 0.56 | 0.02 | 0.57 | |
| fOverlaps | 0.88 | 0.26 | 1.50 | |
| gvizPlot | 7.62 | 0.30 | 12.60 | |
| listPredefinedDataSets | 0 | 0 | 0 | |
| loadAnnotations | 0.24 | 0.00 | 0.25 | |
| makeExampleGRanges | 0.01 | 0.00 | 0.01 | |
| makeExampleOGREDataSet | 0.02 | 0.00 | 0.02 | |
| plotHist | 1.23 | 0.01 | 1.30 | |
| readDataSetFromFolder | 0.27 | 0.00 | 0.32 | |
| subsetGRanges | 0.38 | 0.00 | 0.41 | |
| sumPlot | 2.87 | 0.18 | 5.49 | |
| summarizeOverlap | 0.83 | 0.04 | 1.04 | |