Back to Multiple platform build/check report for BioC 3.17: simplified long |
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This page was generated on 2023-10-16 11:35:20 -0400 (Mon, 16 Oct 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4626 |
palomino3 | Windows Server 2022 Datacenter | x64 | 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" | 4379 |
merida1 | macOS 12.6.4 Monterey | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4395 |
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 598/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
Dune 1.12.0 (landing page) Hector Roux de Bezieux
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
merida1 | macOS 12.6.4 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson2 | macOS 12.6.1 Monterey / arm64 | see weekly results here | ||||||||||||
To the developers/maintainers of the Dune package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Dune.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: Dune |
Version: 1.12.0 |
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:Dune.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings Dune_1.12.0.tar.gz |
StartedAt: 2023-10-15 20:59:35 -0400 (Sun, 15 Oct 2023) |
EndedAt: 2023-10-15 21:04:08 -0400 (Sun, 15 Oct 2023) |
EllapsedTime: 273.7 seconds |
RetCode: 0 |
Status: OK |
CheckDir: Dune.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:Dune.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings Dune_1.12.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/Dune.Rcheck’ * using R version 4.3.1 (2023-06-16) * using platform: x86_64-pc-linux-gnu (64-bit) * R was compiled by gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0 GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0 * running under: Ubuntu 22.04.3 LTS * using session charset: UTF-8 * checking for file ‘Dune/DESCRIPTION’ ... OK * this is package ‘Dune’ version ‘1.12.0’ * 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 ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘Dune’ 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 loading without being on the library search path ... OK * checking startup messages can be suppressed ... OK * checking dependencies in R code ... NOTE package 'methods' is used but not declared * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE .metricTrend: no visible binding for global variable ‘.’ .metricTrend: no visible binding for global variable ‘step’ .metricTrend: no visible binding for global variable ‘change’ .metricTrend: no visible binding for global variable ‘value’ .plotMetric: no visible binding for global variable ‘label2’ .plotMetric: no visible binding for global variable ‘metric’ .plotMetric: no visible binding for global variable ‘label1’ ARIImp : f: no visible binding for global variable ‘cells’ ConfusionEvolution : <anonymous>: no visible binding for global variable ‘Freq’ ConfusionEvolution : <anonymous>: no visible binding for global variable ‘total_x’ ConfusionEvolution : <anonymous>: no visible binding for global variable ‘total_y’ ConfusionEvolution: no visible binding for global variable ‘overlap’ ConfusionEvolution: no visible binding for global variable ‘Freq’ ConfusionEvolution: no visible binding for global variable ‘step’ ConfusionPlot: no visible binding for global variable ‘Freq’ ConfusionPlot: no visible binding for global variable ‘total_x’ ConfusionPlot: no visible binding for global variable ‘total_y’ ConfusionPlot: no visible binding for global variable ‘overlap’ NMIImp : f: no visible binding for global variable ‘cells’ intermediateMat: no visible binding for global variable ‘cells’ plotPrePost: no visible binding for global variable ‘Nb’ Undefined global functions or variables: . Freq Nb cells change label1 label2 metric overlap step total_x total_y value Consider adding importFrom("stats", "step") 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 LazyData ... 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 Dune 5.234 0.052 5.286 * 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 ... ‘Dune.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-3.17-bioc/meat/Dune.Rcheck/00check.log’ for details.
Dune.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL Dune ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-library’ * installing *source* package ‘Dune’ ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** 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 (Dune)
Dune.Rcheck/tests/testthat.Rout
R version 4.3.1 (2023-06-16) -- "Beagle Scouts" Copyright (C) 2023 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(Dune) Dune now uses the Normalized Mutual Informationinstead of the adjusted Rand Index. You can restore the old option bysetting metric'ARI' in the Dune function. > > test_check("Dune") [ FAIL 0 | WARN 2 | SKIP 0 | PASS 452 ] [ FAIL 0 | WARN 2 | SKIP 0 | PASS 452 ] > > proc.time() user system elapsed 64.474 1.425 65.888
Dune.Rcheck/Dune-Ex.timings
name | user | system | elapsed | |
ARIImp | 3.204 | 0.116 | 3.320 | |
ARIs | 0.005 | 0.000 | 0.005 | |
ARItrend | 3.935 | 0.100 | 4.035 | |
ConfusionEvolution | 0 | 0 | 0 | |
ConfusionPlot | 0.222 | 0.003 | 0.226 | |
Dune | 5.234 | 0.052 | 5.286 | |
NMIImp | 2.881 | 0.008 | 2.888 | |
NMIs | 0.005 | 0.000 | 0.005 | |
NMItrend | 3.088 | 0.048 | 3.136 | |
clusterConversion | 2.819 | 0.024 | 2.843 | |
functionTracking | 3.101 | 0.016 | 3.117 | |
intermediateMat | 2.898 | 0.019 | 2.918 | |
plotARIs | 3.218 | 0.036 | 3.254 | |
plotNMIs | 3.113 | 0.000 | 3.113 | |
plotPrePost | 3.042 | 0.024 | 3.066 | |
whenToStop | 2.845 | 0.008 | 2.853 | |