Back to Multiple platform build/check report for BioC 3.14 |
|
This page was generated on 2022-04-13 12:09:00 -0400 (Wed, 13 Apr 2022).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4324 |
tokay2 | Windows Server 2012 R2 Standard | x64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4077 |
machv2 | macOS 10.14.6 Mojave | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4137 |
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 wavClusteR package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/wavClusteR.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 2060/2083 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
wavClusteR 2.28.0 (landing page) Federico Comoglio
| nebbiolo2 | Linux (Ubuntu 20.04.4 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: wavClusteR |
Version: 2.28.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:wavClusteR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings wavClusteR_2.28.0.tar.gz |
StartedAt: 2022-04-12 19:57:33 -0400 (Tue, 12 Apr 2022) |
EndedAt: 2022-04-12 20:04:50 -0400 (Tue, 12 Apr 2022) |
EllapsedTime: 436.7 seconds |
RetCode: 0 |
Status: OK |
CheckDir: wavClusteR.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:wavClusteR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings wavClusteR_2.28.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/wavClusteR.Rcheck’ * using R version 4.1.3 (2022-03-10) * using platform: x86_64-apple-darwin17.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘wavClusteR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘wavClusteR’ version ‘2.28.0’ * checking package namespace information ... OK * checking package dependencies ... NOTE Package which this enhances but not available for checking: ‘doMC’ * 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 for sufficient/correct file permissions ... OK * checking whether package ‘wavClusteR’ 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 ... NOTE 'library' or 'require' call to ‘doMC’ in package code. Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE annotateClusters: no visible binding for global variable ‘Percentage’ annotateClusters: no visible binding for global variable ‘Compartment’ estimateFDR: no visible global function definition for ‘DNAString’ estimateFDR: no visible global function definition for ‘lines’ estimateFDR: no visible global function definition for ‘legend’ estimateFDR: no visible global function definition for ‘axis’ exportGR: no visible global function definition for ‘write.table’ filterClustersCWT: no visible global function definition for ‘DNAString’ filterClustersMRN: no visible global function definition for ‘txtProgressBar’ filterClustersMRN: no visible global function definition for ‘setTxtProgressBar’ getClustersMRN: no visible global function definition for ‘registerDoMC’ getComplSubst: no visible global function definition for ‘DNAStringSet’ getExpInterval: no visible global function definition for ‘par’ getExpInterval: no visible global function definition for ‘lines’ getExpInterval: no visible global function definition for ‘legend’ getExpInterval: no visible global function definition for ‘polygon’ getExpInterval: no visible global function definition for ‘rect’ getExpInterval: no visible global function definition for ‘text’ getLogOdd: no visible global function definition for ‘dbinom’ getMetaCoverage: no visible global function definition for ‘axis’ getMetaGene: no visible global function definition for ‘grid’ getMetaGene: no visible global function definition for ‘axis’ getMetaGene: no visible global function definition for ‘abline’ getMetaTSS: no visible global function definition for ‘grid’ getMetaTSS: no visible global function definition for ‘axis’ plotSizeDistribution: no visible global function definition for ‘hist’ plotStatistics: no visible binding for global variable ‘panel.smooth’ plotStatistics : panelCor: no visible global function definition for ‘par’ plotStatistics : panelCor: no visible global function definition for ‘strwidth’ plotStatistics : panelCor: no visible global function definition for ‘text’ plotStatistics: no visible global function definition for ‘pairs’ plotSubstitutions: no visible global function definition for ‘par’ plotSubstitutions: no visible global function definition for ‘barplot’ processChunk: no visible global function definition for ‘extractAt’ processMD: no visible global function definition for ‘registerDoMC’ readSortedBam: no visible global function definition for ‘scanBamFlag’ readSortedBam : <anonymous>: no visible binding for global variable ‘rname’ readSortedBam : <anonymous>: no visible binding for global variable ‘qwidth’ Undefined global functions or variables: Compartment DNAString DNAStringSet Percentage abline axis barplot dbinom extractAt grid hist legend lines pairs panel.smooth par polygon qwidth rect registerDoMC rname scanBamFlag setTxtProgressBar strwidth text txtProgressBar write.table Consider adding importFrom("graphics", "abline", "axis", "barplot", "grid", "hist", "legend", "lines", "pairs", "panel.smooth", "par", "polygon", "rect", "strwidth", "text") importFrom("stats", "dbinom") importFrom("utils", "setTxtProgressBar", "txtProgressBar", "write.table") 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’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed annotateClusters 11.146 0.231 11.539 filterClusters 7.630 0.040 7.684 plotStatistics 7.319 0.039 7.363 getMetaCoverage 7.318 0.035 7.428 plotSizeDistribution 7.187 0.034 7.246 getMetaGene 7.078 0.030 7.115 getClusters 6.660 0.039 6.708 getHighConfSub 5.471 0.018 5.553 getAllSub 5.361 0.017 5.381 plotSubstitutions 5.125 0.013 5.141 * 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-3.14-bioc/meat/wavClusteR.Rcheck/00check.log’ for details.
wavClusteR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL wavClusteR ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’ * installing *source* package ‘wavClusteR’ ... ** using staged installation ** R ** data ** 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 (wavClusteR)
wavClusteR.Rcheck/wavClusteR-Ex.timings
name | user | system | elapsed | |
FitMixtureModel | 0.078 | 0.006 | 0.090 | |
annotateClusters | 11.146 | 0.231 | 11.539 | |
filterClusters | 7.630 | 0.040 | 7.684 | |
getAllSub | 5.361 | 0.017 | 5.381 | |
getClusters | 6.660 | 0.039 | 6.708 | |
getExpInterval | 0.047 | 0.008 | 0.056 | |
getHighConfSub | 5.471 | 0.018 | 5.553 | |
getMetaCoverage | 7.318 | 0.035 | 7.428 | |
getMetaGene | 7.078 | 0.030 | 7.115 | |
getMetaTSS | 0.273 | 0.006 | 0.280 | |
plotSizeDistribution | 7.187 | 0.034 | 7.246 | |
plotStatistics | 7.319 | 0.039 | 7.363 | |
plotSubstitutions | 5.125 | 0.013 | 5.141 | |
readSortedBam | 0.172 | 0.002 | 0.175 | |