Caleb Lareau
| Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022) |
| git_url: https://git.bioconductor.org/packages/diffloop |
| git_branch: master |
| git_last_commit: 71f41c9 |
| git_last_commit_date: 2022-03-11 11:11:40 -0400 (Fri, 11 Mar 2022) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-03-18 11:07:23 -0400 (Fri, 18 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" | 4097 |
| 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 diffloop package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/diffloop.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 515/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
Caleb Lareau
| 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 | WARNINGS | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| Package: diffloop |
| Version: 1.23.2 |
| Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:diffloop.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings diffloop_1.23.2.tar.gz |
| StartedAt: 2022-03-17 18:56:31 -0400 (Thu, 17 Mar 2022) |
| EndedAt: 2022-03-17 19:00:08 -0400 (Thu, 17 Mar 2022) |
| EllapsedTime: 216.7 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: diffloop.Rcheck |
| Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:diffloop.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings diffloop_1.23.2.tar.gz ### ############################################################################## ############################################################################## * using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/diffloop.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 'diffloop/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'diffloop' version '1.23.2' * 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 ... NOTE Found the following hidden files and directories: .travis.yml These were most likely included in error. See section 'Package structure' in the 'Writing R Extensions' manual. * checking for portable file names ... OK * checking whether package 'diffloop' can be installed ... WARNING Found the following significant warnings: Warning: Package 'diffloop' is deprecated and will be removed from Bioconductor Warning: replacing previous import 'GenomicRanges::windows' by 'grDevices::windows' when loading 'diffloop' See 'D:/biocbuild/bbs-3.15-bioc/meat/diffloop.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 ... 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 * 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/diffloop.Rcheck/00check.log' for details.
diffloop.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL diffloop
###
##############################################################################
##############################################################################
* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'diffloop' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import 'GenomicRanges::windows' by 'grDevices::windows' when loading 'diffloop'
** help
*** installing help indices
converting help for package 'diffloop'
finding HTML links ... done
addchr html
annotateAnchors html
annotateAnchors.bed html
annotateAnchors.bigwig html
annotateLoops html
annotateLoops.dge html
bedToGRanges html
calcLDSizeFactors html
callCCDs html
computeBoundaryScores html
diffloop html
dim-loops-method html
featureTest html
filterLoops html
filterSpanningLoops html
geneinfo html
getHumanGenes html
getHumanTSS html
getMouseGenes html
getMouseTSS html
head-loops-method html
human.genes html
interchromosomal html
intrachromosomal html
keepCTCFloops html
keepEPloops html
loopAssoc html
loopDistancePlot html
loopGenes html
loopMetrics html
loopPlot html
loopWidth html
loops-class html
loops.small html
loopsMake html
loopsMake.mango html
loopsSubset html
mangoCorrection html
manyLoopPlots html
mergeAnchors html
numAnchors html
numLoops html
padGRanges html
pcaPlot html
plotTopLoops html
quickAssoc html
quickAssocVoom html
removeRegion html
removeSelfLoops html
rmchr html
sampleNames-loops-method html
slidingWindowTest html
splitSamples html
sub-loops-numeric-numeric-missing-method
html
subsetLoops html
subsetRegion html
subsetRegionAB html
summary-loops-method html
tail-loops-method html
topLoops html
union-loops-loops-method html
updateLDGroups html
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import 'GenomicRanges::windows' by 'grDevices::windows' when loading 'diffloop'
Warning: Package 'diffloop' is deprecated and will be removed from Bioconductor
version 3.16
** testing if installed package can be loaded from final location
Warning: replacing previous import 'GenomicRanges::windows' by 'grDevices::windows' when loading 'diffloop'
Warning: Package 'diffloop' is deprecated and will be removed from Bioconductor
version 3.16
** testing if installed package keeps a record of temporary installation path
* DONE (diffloop)
Making 'packages.html' ... done
diffloop.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(diffloop)
Warning messages:
1: replacing previous import 'GenomicRanges::windows' by 'grDevices::windows' when loading 'diffloop'
2: Package 'diffloop' is deprecated and will be removed from Bioconductor
version 3.16
>
> test_check("diffloop")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 4 ]
>
> proc.time()
user system elapsed
9.50 0.62 10.07
diffloop.Rcheck/diffloop-Ex.timings
| name | user | system | elapsed | |
| addchr | 0.09 | 0.05 | 0.14 | |
| annotateAnchors | 0.14 | 0.00 | 0.14 | |
| annotateAnchors.bed | 0.08 | 0.00 | 0.08 | |
| annotateAnchors.bigwig | 0.06 | 0.01 | 0.08 | |
| annotateLoops | 0.32 | 0.00 | 0.31 | |
| annotateLoops.dge | 0.22 | 0.00 | 0.22 | |
| bedToGRanges | 0.06 | 0.00 | 0.06 | |
| calcLDSizeFactors | 0 | 0 | 0 | |
| callCCDs | 0 | 0 | 0 | |
| computeBoundaryScores | 0 | 0 | 0 | |
| featureTest | 0 | 0 | 0 | |
| filterLoops | 0.04 | 0.00 | 0.05 | |
| filterSpanningLoops | 0 | 0 | 0 | |
| getHumanGenes | 0.07 | 0.00 | 0.06 | |
| getHumanTSS | 0.14 | 0.02 | 0.16 | |
| getMouseGenes | 0.08 | 0.00 | 0.07 | |
| getMouseTSS | 0.11 | 0.00 | 0.11 | |
| interchromosomal | 0.01 | 0.00 | 0.02 | |
| intrachromosomal | 0.02 | 0.00 | 0.01 | |
| keepCTCFloops | 0.09 | 0.00 | 0.10 | |
| keepEPloops | 0.19 | 0.01 | 0.20 | |
| loopAssoc | 0 | 0 | 0 | |
| loopDistancePlot | 0.01 | 0.00 | 0.02 | |
| loopGenes | 0.10 | 0.00 | 0.09 | |
| loopMetrics | 0 | 0 | 0 | |
| loopPlot | 0.43 | 0.00 | 0.44 | |
| loopWidth | 0 | 0 | 0 | |
| loopsMake | 0.00 | 0.02 | 0.01 | |
| loopsMake.mango | 0 | 0 | 0 | |
| loopsSubset | 0.16 | 0.00 | 0.16 | |
| mangoCorrection | 0.06 | 0.00 | 0.06 | |
| manyLoopPlots | 0.07 | 0.00 | 0.06 | |
| mergeAnchors | 0.06 | 0.03 | 0.09 | |
| numAnchors | 0.00 | 0.01 | 0.02 | |
| numLoops | 0 | 0 | 0 | |
| padGRanges | 0.09 | 0.00 | 0.09 | |
| pcaPlot | 0 | 0 | 0 | |
| plotTopLoops | 0.67 | 0.02 | 0.69 | |
| quickAssoc | 0.04 | 0.00 | 0.03 | |
| quickAssocVoom | 0.01 | 0.00 | 0.02 | |
| removeRegion | 0.14 | 0.01 | 0.15 | |
| removeSelfLoops | 0.02 | 0.00 | 0.02 | |
| rmchr | 0.08 | 0.02 | 0.09 | |
| sampleNames-loops-method | 0 | 0 | 0 | |
| slidingWindowTest | 0 | 0 | 0 | |
| splitSamples | 0.04 | 0.00 | 0.05 | |
| subsetLoops | 0.02 | 0.00 | 0.02 | |
| subsetRegion | 0.31 | 0.01 | 0.32 | |
| subsetRegionAB | 0.20 | 0.00 | 0.21 | |
| summary-loops-method | 0.05 | 0.00 | 0.04 | |
| topLoops | 0.03 | 0.00 | 0.03 | |
| union-loops-loops-method | 0.15 | 0.00 | 0.16 | |
| updateLDGroups | 0 | 0 | 0 | |