Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-12-02 12:04 -0500 (Mon, 02 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4739 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4482 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4510 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4462 |
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 |
Package 2152/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
timeOmics 1.18.0 (landing page) Antoine Bodein
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | WARNINGS | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | WARNINGS | OK | |||||||||
To the developers/maintainers of the timeOmics package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/timeOmics.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
Package: timeOmics |
Version: 1.18.0 |
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:timeOmics.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings timeOmics_1.18.0.tar.gz |
StartedAt: 2024-11-29 07:49:22 -0500 (Fri, 29 Nov 2024) |
EndedAt: 2024-11-29 07:55:39 -0500 (Fri, 29 Nov 2024) |
EllapsedTime: 377.2 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: timeOmics.Rcheck |
Warnings: 2 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:timeOmics.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings timeOmics_1.18.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/timeOmics.Rcheck’ * using R version 4.4.2 (2024-10-31) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 * running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * checking for file ‘timeOmics/DESCRIPTION’ ... OK * this is package ‘timeOmics’ version ‘1.18.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib: cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES' 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 ‘timeOmics’ 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 ... NOTE Problems with news in ‘NEWS.md’: No news entries found. * checking code 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 loading without being on the library search path ... OK * checking whether startup messages can be suppressed ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... WARNING getCluster: function(X, user.block, user.cluster) getCluster.UpDown: function(X, user.block, user.cluster, .by, .preserve, ...) filter: function(.data, ..., .by, .preserve) filter.cluster.df: function(.data, user.block, user.cluster) See section ‘Generic functions and methods’ in the ‘Writing R Extensions’ manual. * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE .mutate_cluster: no visible binding for global variable ‘cluster’ .mutate_cluster: no visible binding for global variable ‘contrib.max’ check_legend.block.name: no visible global function definition for ‘is’ dmatrix.spearman.dissimilarity: no visible global function definition for ‘cor’ filter.cluster.df: no visible binding for global variable ‘block’ filter.cluster.df: no visible binding for global variable ‘cluster’ getCluster.block.pls: no visible binding for global variable ‘block’ getCluster.block.pls: no visible binding for global variable ‘molecule’ getCluster.block.pls: no visible binding for global variable ‘comp’ getCluster.block.spls: no visible binding for global variable ‘block’ getCluster.block.spls: no visible binding for global variable ‘molecule’ getCluster.block.spls: no visible binding for global variable ‘comp’ getCluster.mixo_pls: no visible binding for global variable ‘comp’ getCluster.mixo_spls: no visible binding for global variable ‘comp’ getCluster.pca: no visible binding for global variable ‘comp’ getCluster.spca: no visible binding for global variable ‘comp’ getNcomp: no visible global function definition for ‘is’ getUpDownCluster: no visible global function definition for ‘is’ get_MSE: no visible binding for global variable ‘feature’ get_MSE: no visible global function definition for ‘na.omit’ get_MSE: no visible binding for global variable ‘Y_i’ get_MSE: no visible binding for global variable ‘Y_hat’ get_MSE: no visible binding for global variable ‘error’ lmms.filter.lines: no visible global function definition for ‘is’ lmms.filter.lines: no visible global function definition for ‘slot’ lmms.filter.lines: no visible binding for global variable ‘feature’ lmms.filter.lines: no visible binding for global variable ‘BP.test’ lmms.filter.lines: no visible binding for global variable ‘MSE’ lmms.filter.lines: no visible binding for global variable ‘val’ lmms.filter.lines: no visible global function definition for ‘all_of’ plot.ncomp.tune.silhouette: no visible global function definition for ‘is’ plot.ncomp.tune.silhouette: no visible binding for global variable ‘ncomp’ plot.proportionality: no visible binding for global variable ‘cluster1’ plot.proportionality: no visible binding for global variable ‘value’ plot.proportionality: no visible binding for global variable ‘insideout’ plot.spca.tune.silhouette: no visible binding for global variable ‘comp’ plot.spca.tune.silhouette: no visible binding for global variable ‘X’ plot.spca.tune.silhouette: no visible binding for global variable ‘na.omit’ plot.spca.tune.silhouette: no visible binding for global variable ‘contrib’ plot.spca.tune.silhouette: no visible binding for global variable ‘value’ plotLong: no visible binding for global variable ‘block’ plotLong: no visible binding for global variable ‘new.block’ plotLong: no visible global function definition for ‘is’ plotLong: no visible binding for global variable ‘.’ plotLong: no visible binding for global variable ‘value’ plotLong: no visible binding for global variable ‘molecule’ proportionality: no visible binding for global variable ‘molecule’ proportionality: no visible binding for global variable ‘cluster’ proportionality: no visible binding for global variable ‘.’ proportionality : <anonymous>: no visible binding for global variable ‘.’ proportionality: no visible binding for global variable ‘feature1’ proportionality: no visible binding for global variable ‘feature2’ proportionality: no visible binding for global variable ‘cluster1’ proportionality: no visible binding for global variable ‘cluster2’ proportionality: no visible global function definition for ‘na.omit’ remove.low.cv: no visible global function definition for ‘is’ remove.low.cv : <anonymous>: no visible global function definition for ‘sd’ sd_new: no visible global function definition for ‘sd’ silhouette: no visible binding for global variable ‘silhouette.coef’ stat_median: no visible binding for global variable ‘cluster1’ stat_median: no visible binding for global variable ‘cluster2’ stat_median: no visible binding for global variable ‘value’ stat_median: no visible global function definition for ‘median’ stat_median: no visible binding for global variable ‘Pvalue’ stat_median: no visible binding for global variable ‘na.omit’ to_lr2phs: no visible global function definition for ‘var’ tune.silhouette.get_choice_keepX: no visible binding for global variable ‘comp’ tune.silhouette.get_choice_keepX: no visible binding for global variable ‘direction’ tune.silhouette.get_choice_keepX: no visible binding for global variable ‘Pval.pos’ tune.silhouette.get_choice_keepX: no visible binding for global variable ‘Pval.neg’ tune.silhouette.get_choice_keepX: no visible binding for global variable ‘distance_from_origin’ tune.silhouette.get_choice_keepX: no visible binding for global variable ‘Pval.dir’ tune.silhouette.get_choice_keepX: no visible binding for global variable ‘Pval.value’ tune.silhouette.get_choice_keepX: no visible global function definition for ‘na.omit’ tune.silhouette.get_choice_keepX : <anonymous>: no visible binding for global variable ‘Pval.value’ tune.silhouette.get_choice_keepX : <anonymous>: no visible binding for global variable ‘distance_from_origin’ tune.silhouette.get_choice_keepX : <anonymous>: no visible binding for global variable ‘.’ tune.silhouette.get_slopes: no visible global function definition for ‘is’ tune.silhouette.get_slopes: no visible binding for global variable ‘origin’ tune.silhouette.get_slopes: no visible binding for global variable ‘destination’ tune.silhouette.get_slopes: no visible binding for global variable ‘.’ tune.silhouette.get_slopes: no visible binding for global variable ‘comp’ tune.silhouette.get_slopes: no visible binding for global variable ‘direction’ tune.silhouette.get_slopes: no visible binding for global variable ‘slope.pos’ tune.silhouette.get_slopes: no visible binding for global variable ‘slope.neg’ tune.silhouette.get_slopes: no visible binding for global variable ‘Z_score.pos’ tune.silhouette.get_slopes: no visible global function definition for ‘pnorm’ tune.silhouette.get_slopes: no visible binding for global variable ‘Z_score.neg’ tuneCluster.block.spls: no visible binding for global variable ‘silhouette.coef’ tuneCluster.spca: no visible binding for global variable ‘silhouette.coef’ tuneCluster.spls: no visible binding for global variable ‘silhouette.coef’ unscale: no visible global function definition for ‘is’ Undefined global functions or variables: . BP.test MSE Pval.dir Pval.neg Pval.pos Pval.value Pvalue X Y_hat Y_i Z_score.neg Z_score.pos all_of block cluster cluster1 cluster2 comp contrib contrib.max cor destination direction distance_from_origin error feature feature1 feature2 insideout is median molecule na.omit ncomp new.block origin pnorm sd silhouette.coef slope.neg slope.pos slot val value var Consider adding importFrom("methods", "is", "slot") importFrom("stats", "cor", "median", "na.omit", "pnorm", "sd", "var") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods'). * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... WARNING Undocumented code objects: ‘timeOmics.simdata’ Undocumented data sets: ‘timeOmics.simdata’ All user-level objects in a package should have documentation entries. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * 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 LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking R/sysdata.rda ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed tuneCluster.block.spls 11.691 0.126 11.818 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 2 WARNINGs, 3 NOTEs See ‘/home/biocbuild/bbs-3.20-bioc/meat/timeOmics.Rcheck/00check.log’ for details.
timeOmics.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL timeOmics ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’ * installing *source* package ‘timeOmics’ ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading Note: wrong number of arguments to '*' ** help *** installing help indices *** copying figures ** 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 (timeOmics)
timeOmics.Rcheck/tests/testthat.Rout
R version 4.4.2 (2024-10-31) -- "Pile of Leaves" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu 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(timeOmics) Loading required package: mixOmics Loading required package: MASS Loading required package: lattice Loading required package: ggplot2 Loaded mixOmics 6.30.0 Thank you for using mixOmics! Tutorials: http://mixomics.org Bookdown vignette: https://mixomicsteam.github.io/Bookdown Questions, issues: Follow the prompts at http://mixomics.org/contact-us Cite us: citation('mixOmics') > > test_check("timeOmics") [ FAIL 0 | WARN 0 | SKIP 0 | PASS 263 ] > > proc.time() user system elapsed 52.477 0.708 53.175
timeOmics.Rcheck/timeOmics-Ex.timings
name | user | system | elapsed | |
getCluster | 0.334 | 0.020 | 0.354 | |
getNcomp | 2.593 | 0.083 | 2.676 | |
getSilhouette | 1.521 | 0.045 | 1.568 | |
getUpDownCluster | 0.268 | 0.005 | 0.274 | |
get_demo_cluster | 0.186 | 0.001 | 0.188 | |
get_demo_silhouette | 0.001 | 0.000 | 0.001 | |
lmms.filter.lines | 0.104 | 0.016 | 0.119 | |
plotLong | 2.039 | 0.045 | 2.083 | |
proportionality | 2.531 | 0.022 | 2.553 | |
remove.low.cv | 0.001 | 0.000 | 0.001 | |
tuneCluster.block.spls | 11.691 | 0.126 | 11.818 | |
tuneCluster.spca | 1.804 | 0.007 | 1.812 | |
tuneCluster.spls | 2.208 | 0.022 | 2.231 | |
unscale | 0 | 0 | 0 | |