Back to Multiple platform build/check report for BioC 3.13 |
|
This page was generated on 2021-10-15 15:06:38 -0400 (Fri, 15 Oct 2021).
To the developers/maintainers of the hiAnnotator package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/hiAnnotator.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 854/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
hiAnnotator 1.26.0 (landing page) Nirav V Malani
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |||||||||
Package: hiAnnotator |
Version: 1.26.0 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:hiAnnotator.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings hiAnnotator_1.26.0.tar.gz |
StartedAt: 2021-10-14 19:57:15 -0400 (Thu, 14 Oct 2021) |
EndedAt: 2021-10-14 20:02:53 -0400 (Thu, 14 Oct 2021) |
EllapsedTime: 337.4 seconds |
RetCode: 0 |
Status: OK |
CheckDir: hiAnnotator.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:hiAnnotator.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings hiAnnotator_1.26.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/hiAnnotator.Rcheck’ * using R version 4.1.1 (2021-08-10) * using platform: x86_64-apple-darwin17.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘hiAnnotator/DESCRIPTION’ ... OK * this is package ‘hiAnnotator’ version ‘1.26.0’ * 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: .git_fetch_output.txt .git_merge_output.txt 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 ‘hiAnnotator’ 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 ... NOTE get2NearestFeature: no visible global function definition for ‘IRanges’ get2NearestFeature: no visible global function definition for ‘mid’ get2NearestFeature: no visible binding for global variable ‘dist’ get2NearestFeature: no visible binding for global variable ‘qStrand’ get2NearestFeature: no visible binding for global variable ‘subjectHits’ get2NearestFeature : <anonymous>: no visible binding for global variable ‘queryHits’ get2NearestFeature : <anonymous>: no visible binding for global variable ‘dist’ get2NearestFeature : <anonymous>: no visible binding for global variable ‘featureName’ getFeatureCounts : <anonymous>: no visible global function definition for ‘countQueryHits’ getFeatureCountsBig: no visible global function definition for ‘mid’ getLowestDists: no visible binding for global variable ‘queryHits’ getLowestDists: no visible binding for global variable ‘dist’ getNearestFeature: no visible global function definition for ‘IRanges’ getNearestFeature: no visible global function definition for ‘mid’ getNearestFeature: no visible binding for global variable ‘queryHits’ getNearestFeature: no visible binding for global variable ‘n’ getNearestFeature: no visible binding for global variable ‘featureName’ getNearestFeature: no visible binding for global variable ‘dist’ getSitesInFeature: no visible global function definition for ‘overlapsAny’ getSitesInFeature: no visible binding for global variable ‘queryHits’ getSitesInFeature: no visible global function definition for ‘n’ getSitesInFeature: no visible binding for global variable ‘featureName’ makeChunks: no visible global function definition for ‘breakInChunks’ makeChunks: no visible global function definition for ‘detectCores’ makeChunks : <anonymous>: no visible global function definition for ‘keepSeqlevels’ makeChunks : <anonymous>: no visible global function definition for ‘seqlevelsInUse’ makeGRanges: no visible global function definition for ‘IRanges’ makeGRanges: no visible global function definition for ‘seqlengths’ makeGRanges: no visible global function definition for ‘seqlevels<-’ makeGRanges: no visible global function definition for ‘sortSeqlevels’ makeGRanges: no visible global function definition for ‘seqlevelsInUse’ makeGRanges: no visible global function definition for ‘seqlengths<-’ makeGRanges: no visible global function definition for ‘seqlevels’ Undefined global functions or variables: IRanges breakInChunks countQueryHits detectCores dist featureName keepSeqlevels mid n overlapsAny qStrand queryHits seqlengths seqlengths<- seqlevels seqlevels<- seqlevelsInUse sortSeqlevels subjectHits Consider adding importFrom("stats", "dist") to your NAMESPACE file. * 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 contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking files in ‘vignettes’ ... NOTE The following directory looks like a leftover from 'knitr': ‘figure’ Please remove from your package. * checking examples ... 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: 3 NOTEs See ‘/Users/biocbuild/bbs-3.13-bioc/meat/hiAnnotator.Rcheck/00check.log’ for details.
hiAnnotator.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL hiAnnotator ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’ * installing *source* package ‘hiAnnotator’ ... ** using staged installation ** R ** data ** 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 (hiAnnotator)
hiAnnotator.Rcheck/hiAnnotator-Ex.timings
name | user | system | elapsed | |
cleanColname | 0.002 | 0.001 | 0.002 | |
doAnnotation | 2.358 | 0.056 | 2.416 | |
get2NearestFeature | 2.336 | 0.076 | 2.414 | |
getFeatureCounts | 0.999 | 0.008 | 1.008 | |
getFeatureCountsBig | 0.941 | 0.010 | 0.951 | |
getLowestDists | 0.144 | 0.000 | 0.145 | |
getNearestFeature | 2.995 | 0.061 | 3.059 | |
getRelevantCol | 0.007 | 0.002 | 0.009 | |
getSitesInFeature | 1.108 | 0.018 | 1.128 | |
getUCSCtable | 0.000 | 0.000 | 0.001 | |
getWindowLabel | 0.001 | 0.000 | 0.001 | |
makeChunks | 0.571 | 0.009 | 0.580 | |
makeGRanges | 0.618 | 0.011 | 0.631 | |
makeUCSCsession | 0 | 0 | 0 | |
plotdisFeature | 1.699 | 0.026 | 1.728 | |