Back to Multiple platform build/check report for BioC 3.14 |
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This page was generated on 2022-04-13 12:06:26 -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 deltaGseg package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/deltaGseg.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 483/2083 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
deltaGseg 1.34.0 (landing page) Diana Low
| 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: deltaGseg |
Version: 1.34.0 |
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe --arch x64 CMD check --no-multiarch --install=check:deltaGseg.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings deltaGseg_1.34.0.tar.gz |
StartedAt: 2022-04-12 18:26:20 -0400 (Tue, 12 Apr 2022) |
EndedAt: 2022-04-12 18:30:48 -0400 (Tue, 12 Apr 2022) |
EllapsedTime: 267.7 seconds |
RetCode: 0 |
Status: OK |
CheckDir: deltaGseg.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe --arch x64 CMD check --no-multiarch --install=check:deltaGseg.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings deltaGseg_1.34.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/deltaGseg.Rcheck' * using R version 4.1.3 (2022-03-10) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'deltaGseg/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'deltaGseg' version '1.34.0' * checking package namespace information ... OK * checking package dependencies ... NOTE Depends: includes the non-default packages: 'ggplot2', 'changepoint', 'wavethresh', 'tseries', 'pvclust', 'fBasics', 'grid', 'reshape', 'scales' Adding so many packages to the search path is excessive and importing selectively is preferable. * 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: .BBSoptions 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 'deltaGseg' can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking 'build' directory ... OK * checking DESCRIPTION meta-information ... NOTE Malformed Description field: should contain one or more complete sentences. * 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 boot.hclust_new: no visible global function definition for 'hclust' dist.pvclust: no visible global function definition for 'as.dist' dist.pvclust: no visible global function definition for 'cor' dist.pvclust: no visible global function definition for 'na.omit' dist.pvclust: no visible global function definition for 'dist' distw.pvclust: no visible global function definition for 'as.dist' mydist: no visible global function definition for 'dist' mydist: no visible global function definition for 'as.dist' parseTraj: no visible global function definition for 'read.table' pvclust_new: no visible global function definition for 'hclust' segden1: no visible global function definition for 'quantile' text.pvclust: no visible global function definition for 'par' text.pvclust: no visible global function definition for 'text' clusterSegments,SegTrajectories: no visible global function definition for 'hclust' clusterSegments,SegTrajectories: no visible global function definition for 'layout' clusterSegments,SegTrajectories: no visible global function definition for 'lines' clusterSegments,SegTrajectories: no visible global function definition for 'points' clusterSegments,SegTrajectories: no visible global function definition for 'abline' clusterSegments,SegTrajectories: no visible global function definition for 'text' clusterSegments,SegTrajectories: no visible global function definition for 'identify' clusterSegments,SegTrajectories: no visible global function definition for 'par' clusterSegments,SegTrajectories: no visible global function definition for 'locator' clusterSegments,SegTrajectories: no visible global function definition for 'cutree' clusterSegments,SegTrajectories: no visible global function definition for 'mtext' clusterSegments,SegTrajectories: no visible global function definition for 'median' denoiseSegments,Trajectories: no visible global function definition for 'txtProgressBar' denoiseSegments,Trajectories: no visible global function definition for 'setTxtProgressBar' diagnosticPlots,SegSeriesTrajectories: no visible binding for global variable 'residuals' diagnosticPlots,SegSeriesTrajectories: no visible global function definition for 'acf' diagnosticPlots,SegSeriesTrajectories: no visible global function definition for 'qnorm' diagnosticPlots,SegSeriesTrajectories: no visible binding for global variable 'lag' Undefined global functions or variables: abline acf as.dist cor cutree dist hclust identify lag layout lines locator median mtext na.omit par points qnorm quantile read.table residuals setTxtProgressBar text txtProgressBar Consider adding importFrom("graphics", "abline", "identify", "layout", "lines", "locator", "mtext", "par", "points", "text") importFrom("stats", "acf", "as.dist", "cor", "cutree", "dist", "hclust", "lag", "median", "na.omit", "qnorm", "quantile", "residuals") importFrom("utils", "read.table", "setTxtProgressBar", "txtProgressBar") 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 installed files from 'inst/doc' ... NOTE The following files should probably not be installed: 'diagplots.png', 'simclust.png', 'simtraj.png', 'simtrajtr.png', 'simtrajtr2.png', 'traj1.png', 'traj1break.png', 'traj1ss0.png', 'traj1ss1.png', 'traj1tr.png' Consider the use of a .Rinstignore file: see 'Writing R Extensions', or move the vignette sources from 'inst/doc' to 'vignettes'. * checking files in 'vignettes' ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed clusterPV 159.19 25.86 185.08 * 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: 5 NOTEs See 'C:/Users/biocbuild/bbs-3.14-bioc/meat/deltaGseg.Rcheck/00check.log' for details.
deltaGseg.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe --arch x64 CMD INSTALL --no-multiarch deltaGseg ### ############################################################################## ############################################################################## * installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library' * installing *source* package 'deltaGseg' ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'deltaGseg' finding HTML links ... done SegSeriesTrajectories-class html SegTrajectories-class html Trajectories-class html TransTrajectories-class html chooseBreaks-methods html chooseBreaks html clusterPV-methods html clusterPV html clusterSegments-methods html clusterSegments html deltaGseg-package html denoiseSegments-methods html denoiseSegments html diagnosticPlots-methods html diagnosticPlots html getAVD-methods html getAVD html getBreaks-methods html getBreaks html getIntervals-methods html getIntervals html getSegments-methods html getSegments html getTNames-methods html getTNames html getTraj-methods html getTraj html parseTraj html plot-methods html plotDiff-methods html plotDiff html pvals html finding level-2 HTML links ... done show-methods html simtraj html simtraj.tr html simtraj.tr2 html splitTraj-methods html splitTraj html traj1 html traj1.denoise html traj1.ss html traj1.tr html transformSeries-methods html transformSeries html ** building package indices ** installing vignettes 'deltaGseg.Rnw' ** 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 (deltaGseg) Making 'packages.html' ... done
deltaGseg.Rcheck/deltaGseg-Ex.timings
name | user | system | elapsed | |
SegSeriesTrajectories-class | 0.01 | 0.00 | 0.01 | |
SegTrajectories-class | 0 | 0 | 0 | |
Trajectories-class | 0 | 0 | 0 | |
TransTrajectories-class | 0 | 0 | 0 | |
chooseBreaks | 0.07 | 0.02 | 0.09 | |
clusterPV-methods | 0 | 0 | 0 | |
clusterPV | 159.19 | 25.86 | 185.08 | |
clusterSegments-methods | 0 | 0 | 0 | |
clusterSegments | 0 | 0 | 0 | |
denoiseSegments-methods | 0 | 0 | 0 | |
denoiseSegments | 0.54 | 0.05 | 0.59 | |
diagnosticPlots-methods | 0 | 0 | 0 | |
diagnosticPlots | 0.52 | 0.00 | 0.52 | |
getAVD | 0.05 | 0.01 | 0.06 | |
getBreaks-methods | 0 | 0 | 0 | |
getBreaks | 0.06 | 0.02 | 0.08 | |
getIntervals-methods | 0 | 0 | 0 | |
getIntervals | 0.06 | 0.01 | 0.08 | |
getSegments-methods | 0 | 0 | 0 | |
getSegments | 0.05 | 0.02 | 0.06 | |
getTNames-methods | 0 | 0 | 0 | |
getTNames | 0.06 | 0.03 | 0.09 | |
getTraj | 0.05 | 0.02 | 0.06 | |
parseTraj | 0.11 | 0.01 | 0.24 | |
plotDiff-methods | 0 | 0 | 0 | |
plotDiff | 0.53 | 0.03 | 0.57 | |
splitTraj-methods | 0 | 0 | 0 | |
splitTraj | 0.06 | 0.00 | 0.06 | |
transformSeries-methods | 0 | 0 | 0 | |
transformSeries | 0.07 | 0.03 | 0.10 | |