Back to Multiple platform build/check report for BioC 3.16: simplified long |
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This page was generated on 2023-03-20 11:05:18 -0400 (Mon, 20 Mar 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.2 (2022-10-31) -- "Innocent and Trusting" | 4516 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.2.2 (2022-10-31 ucrt) -- "Innocent and Trusting" | 4295 |
lconway | macOS 12.5.1 Monterey | x86_64 | 4.2.2 (2022-10-31) -- "Innocent and Trusting" | 4324 |
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 timeOmics package: - Please 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 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 2050/2183 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
timeOmics 1.10.0 (landing page) Antoine Bodein
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.5.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
Package: timeOmics |
Version: 1.10.0 |
Command: /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:timeOmics.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/library --timings timeOmics_1.10.0.tar.gz |
StartedAt: 2023-03-18 00:35:55 -0400 (Sat, 18 Mar 2023) |
EndedAt: 2023-03-18 00:39:20 -0400 (Sat, 18 Mar 2023) |
EllapsedTime: 204.7 seconds |
RetCode: 0 |
Status: OK |
CheckDir: timeOmics.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:timeOmics.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/library --timings timeOmics_1.10.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.16-bioc/meat/timeOmics.Rcheck’ * using R version 4.2.2 (2022-10-31) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * checking for file ‘timeOmics/DESCRIPTION’ ... OK * this is package ‘timeOmics’ version ‘1.10.0’ * package encoding: UTF-8 * 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 ‘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 ... 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 .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.getCluster: no visible binding for global variable ‘block’ filter.getCluster: 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’ 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’ 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 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 Consider adding importFrom("methods", "is", "slot") importFrom("stats", "cor", "median", "na.omit", "pnorm", "sd") 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 ... 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 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 19.661 0.12 19.781 * 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 ... ‘vignette.Rmd’ using ‘UTF-8’... OK NONE * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 2 NOTEs See ‘/home/biocbuild/bbs-3.16-bioc/meat/timeOmics.Rcheck/00check.log’ for details.
timeOmics.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD INSTALL timeOmics ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.16-bioc/R/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 4.2.2 (2022-10-31) -- "Innocent and Trusting" Copyright (C) 2022 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(timeOmics) Loading required package: mixOmics Loading required package: MASS Loading required package: lattice Loading required package: ggplot2 Loaded mixOmics 6.22.0 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 2 | SKIP 0 | PASS 263 ] [ FAIL 0 | WARN 2 | SKIP 0 | PASS 263 ] > > proc.time() user system elapsed 69.933 0.758 70.676
timeOmics.Rcheck/timeOmics-Ex.timings
name | user | system | elapsed | |
getCluster | 0.878 | 0.068 | 0.945 | |
getNcomp | 2.943 | 0.060 | 3.003 | |
getSilhouette | 1.883 | 0.016 | 1.900 | |
getUpDownCluster | 0.274 | 0.016 | 0.290 | |
get_demo_cluster | 0.210 | 0.004 | 0.214 | |
get_demo_silhouette | 0.001 | 0.000 | 0.001 | |
lmms.filter.lines | 0.160 | 0.004 | 0.163 | |
plotLong | 2.419 | 0.036 | 2.455 | |
proportionality | 2.579 | 0.016 | 2.595 | |
remove.low.cv | 0.001 | 0.000 | 0.001 | |
tuneCluster.block.spls | 19.661 | 0.120 | 19.781 | |
tuneCluster.spca | 2.830 | 0.012 | 2.842 | |
tuneCluster.spls | 3.986 | 0.012 | 3.999 | |
unscale | 0.001 | 0.000 | 0.001 | |