Caleb Lareau
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/diffloop |
| Branch: RELEASE_3_9 |
| Last Commit: 4a91b22 |
| Last Changed Date: 2019-05-02 11:54:02 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:08:54 -0400 (Wed, 16 Oct 2019).
| Package 437/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| diffloop 1.12.0 Caleb Lareau
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: diffloop |
| Version: 1.12.0 |
| Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:diffloop.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings diffloop_1.12.0.tar.gz |
| StartedAt: 2019-10-16 01:11:56 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 01:16:13 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 256.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: diffloop.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:diffloop.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings diffloop_1.12.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/diffloop.Rcheck’ * using R version 3.6.1 (2019-07-05) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘diffloop/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘diffloop’ version ‘1.12.0’ * 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 for sufficient/correct file permissions ... OK * checking whether package ‘diffloop’ 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 * 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 NOTE See ‘/home/biocbuild/bbs-3.9-bioc/meat/diffloop.Rcheck/00check.log’ for details.
diffloop.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL diffloop ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’ * installing *source* package ‘diffloop’ ... ** 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 (diffloop)
diffloop.Rcheck/tests/testthat.Rout
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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(diffloop)
>
> test_check("diffloop")
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 4 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
12.952 0.408 13.367
diffloop.Rcheck/diffloop-Ex.timings
| name | user | system | elapsed | |
| addchr | 0.142 | 0.000 | 0.142 | |
| annotateAnchors | 0.102 | 0.000 | 0.121 | |
| annotateAnchors.bed | 0.059 | 0.004 | 0.063 | |
| annotateAnchors.bigwig | 0.044 | 0.000 | 0.045 | |
| annotateLoops | 0.473 | 0.000 | 0.483 | |
| annotateLoops.dge | 0.877 | 0.008 | 0.886 | |
| bedToGRanges | 0.057 | 0.000 | 0.056 | |
| calcLDSizeFactors | 0.002 | 0.000 | 0.001 | |
| callCCDs | 0.001 | 0.000 | 0.001 | |
| computeBoundaryScores | 0.000 | 0.000 | 0.001 | |
| featureTest | 0.001 | 0.000 | 0.000 | |
| filterLoops | 0.038 | 0.000 | 0.038 | |
| filterSpanningLoops | 0.007 | 0.000 | 0.008 | |
| getHumanGenes | 0.04 | 0.00 | 0.04 | |
| getHumanTSS | 0.102 | 0.008 | 0.111 | |
| getMouseGenes | 0.079 | 0.000 | 0.079 | |
| getMouseTSS | 0.084 | 0.000 | 0.084 | |
| interchromosomal | 0.009 | 0.000 | 0.009 | |
| intrachromosomal | 0.008 | 0.000 | 0.008 | |
| keepCTCFloops | 0.073 | 0.000 | 0.073 | |
| keepEPloops | 0.208 | 0.000 | 0.208 | |
| loopAssoc | 0.002 | 0.000 | 0.002 | |
| loopDistancePlot | 0.022 | 0.000 | 0.022 | |
| loopGenes | 0.125 | 0.000 | 0.125 | |
| loopMetrics | 0.004 | 0.000 | 0.004 | |
| loopPlot | 1.033 | 0.068 | 1.113 | |
| loopWidth | 0.011 | 0.000 | 0.011 | |
| loopsMake | 0.001 | 0.000 | 0.019 | |
| loopsMake.mango | 0.000 | 0.000 | 0.001 | |
| loopsSubset | 0.189 | 0.000 | 0.190 | |
| mangoCorrection | 0.089 | 0.000 | 0.089 | |
| manyLoopPlots | 0.063 | 0.000 | 0.063 | |
| mergeAnchors | 0.088 | 0.000 | 0.088 | |
| numAnchors | 0.01 | 0.00 | 0.01 | |
| numLoops | 0.003 | 0.000 | 0.003 | |
| padGRanges | 0.103 | 0.004 | 0.107 | |
| pcaPlot | 0.020 | 0.004 | 0.024 | |
| plotTopLoops | 0.737 | 0.028 | 0.769 | |
| quickAssoc | 0.031 | 0.000 | 0.030 | |
| quickAssocVoom | 0.03 | 0.00 | 0.03 | |
| removeRegion | 0.127 | 0.000 | 0.128 | |
| removeSelfLoops | 0.005 | 0.000 | 0.005 | |
| rmchr | 0.095 | 0.000 | 0.095 | |
| sampleNames-loops-method | 0.002 | 0.000 | 0.002 | |
| slidingWindowTest | 0.001 | 0.000 | 0.001 | |
| splitSamples | 0.054 | 0.000 | 0.054 | |
| subsetLoops | 0.013 | 0.000 | 0.013 | |
| subsetRegion | 0.567 | 0.004 | 0.583 | |
| subsetRegionAB | 0.199 | 0.000 | 0.199 | |
| summary-loops-method | 0.057 | 0.000 | 0.056 | |
| topLoops | 0.040 | 0.000 | 0.041 | |
| union-loops-loops-method | 0.099 | 0.004 | 0.103 | |
| updateLDGroups | 0.001 | 0.000 | 0.001 | |