Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-11-09 21:30 -0500 (Sat, 09 Nov 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4505 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4506 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4538 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4486 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4493 |
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 492/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
CytoMDS 1.2.0 (landing page) Philippe Hauchamps
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | ERROR | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
To the developers/maintainers of the CytoMDS package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/CytoMDS.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: CytoMDS |
Version: 1.2.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:CytoMDS.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings CytoMDS_1.2.0.tar.gz |
StartedAt: 2024-11-09 00:14:57 -0500 (Sat, 09 Nov 2024) |
EndedAt: 2024-11-09 00:20:41 -0500 (Sat, 09 Nov 2024) |
EllapsedTime: 343.5 seconds |
RetCode: 0 |
Status: OK |
CheckDir: CytoMDS.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:CytoMDS.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings CytoMDS_1.2.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/CytoMDS.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Ventura 13.6.7 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘CytoMDS/DESCRIPTION’ ... OK * this is package ‘CytoMDS’ version ‘1.2.0’ * 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 ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘CytoMDS’ 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 ... NOTE File LICENSE is not mentioned in the DESCRIPTION file. * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * 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 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 ... OK * 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 files in ‘vignettes’ ... OK * checking examples ... OK * 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 running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 1 NOTE See ‘/Users/biocbuild/bbs-3.20-bioc/meat/CytoMDS.Rcheck/00check.log’ for details.
CytoMDS.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL CytoMDS ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’ * installing *source* package ‘CytoMDS’ ... ** using staged installation ** R ** 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 (CytoMDS)
CytoMDS.Rcheck/tests/testthat.Rout
R version 4.4.1 (2024-06-14) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-apple-darwin20 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. > # CytoMDS - Copyright (C) <2023-2024> > # <Université catholique de Louvain (UCLouvain), Belgique> > # > # Description and complete License: see LICENSE file. > # > # This program (CytoMDS) is free software: > # you can redistribute it and/or modify it under the terms of the GNU General > # Public License as published by the Free Software Foundation, > # either version 3 of the License, or (at your option) any later version. > # > # This program is distributed in the hope that it will be useful, > # but WITHOUT ANY WARRANTY; without even the implied warranty of > # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the > # GNU General Public License for more details (<http://www.gnu.org/licenses/>). > > # This file is part of the standard setup for testthat. > # It is recommended that you do not modify it. > # > # Where should you do additional test configuration? > # Learn more about the roles of various files in: > # * https://r-pkgs.org/tests.html > # * https://testthat.r-lib.org/reference/test_package.html#special-files > > library(testthat) > library(CytoMDS) > > test_check("CytoMDS") | | | 0% | |=================================== | 50% | |======================================================================| 100% | | | 0% | |======================================================================| 100% | | | 0% | |=================================== | 50% | |======================================================================| 100% | | | 0% | |================== | 25% | |=================================== | 50% | |==================================================== | 75% | 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|================== | 25% | |=================================== | 50% | |==================================================== | 75% | |======================================================================| 100% [ FAIL 0 | WARN 0 | SKIP 3 | PASS 307 ] ══ Skipped tests (3) ═══════════════════════════════════════════════════════════ • On CRAN (3): 'test-ggplots.R:67:5', 'test-ggplots.R:184:5', 'test-ggplots.R:617:5' [ FAIL 0 | WARN 0 | SKIP 3 | PASS 307 ] Deleting unused snapshots: • ggplots/ggplotmarginaldensities-nothing.svg • ggplots/ggplotmarginaldensities-with-channels-with-translist.svg • ggplots/ggplotmarginaldensities-with-flowframe.svg • ggplots/ggplotmarginaldensities-with-groupby-and-colourby.svg • ggplots/ggplotmarginaldensities-with-groupby-and-same-colourby.svg • ggplots/ggplotmarginaldensities-with-groupby.svg • ggplots/ggplotmarginaldensities-with-sample-subset.svg • ggplots/ggplotmarginaldensities-with-subsampling.svg • ggplots/ggplotsamplemds-arrowthreshold-subset.svg • ggplots/ggplotsamplemds-arrowthreshold.svg • ggplots/ggplotsamplemds-axes-1-2-biplot-arrow-label-size.svg • ggplots/ggplotsamplemds-axes-1-2-biplot-regression-nas.svg • ggplots/ggplotsamplemds-axes-1-2-biplot-regression.svg • ggplots/ggplotsamplemds-axes-3-4-biplot-regression.svg • ggplots/ggplotsamplemds-minimal-call.svg • ggplots/ggplotsamplemds-no-arrow-label.svg • ggplots/ggplotsamplemds-no-point-labels.svg • ggplots/ggplotsamplemds-with-axes-1-and-2-and-extvars-invalid.svg • ggplots/ggplotsamplemds-with-axes-1-and-2-and-extvars-nas.svg • ggplots/ggplotsamplemds-with-axes-1-and-2-and-extvars.svg • ggplots/ggplotsamplemds-with-axes-1-and-2-explicit-labels.svg • ggplots/ggplotsamplemds-with-axes-1-and-2-no-labels.svg • ggplots/ggplotsamplemds-with-axes-1-and-2-real.svg • ggplots/ggplotsamplemds-with-axes-3-and-4-and-extvars.svg • ggplots/ggplotsamplemds-with-axes-3-and-4.svg • ggplots/ggplotsamplemds-with-flipx-y.svg • ggplots/ggplotsamplemds-with-flipx.svg • ggplots/ggplotsamplemds-with-pointlabelsize.svg • ggplots/ggplotsamplemds-with-sizereflectingstress.svg • ggplots/ggplotsamplemdsshepard-with-3-dimensions.svg • ggplots/ggplotsamplemdsshepard-with-default-dim-nb.svg • ggplots/ggplotsamplemdsshepard-with-explicit-graphical-params.svg • ggplots/ggplotsampmds-with-bipl-flpx-y.svg > > proc.time() user system elapsed 35.365 0.554 81.565
CytoMDS.Rcheck/CytoMDS-Ex.timings
name | user | system | elapsed | |
EMDDist | 0.189 | 0.007 | 0.199 | |
MDS | 0.645 | 0.038 | 0.683 | |
channelSummaryStats | 0.768 | 0.005 | 0.773 | |
computeMetricMDS | 0.868 | 0.006 | 0.875 | |
ggplotMarginalDensities | 0.523 | 0.012 | 0.535 | |
ggplotSampleMDS | 1.707 | 0.009 | 1.715 | |
ggplotSampleMDSShepard | 0.920 | 0.007 | 0.927 | |
ggplotSampleMDSWrapBiplots | 1.731 | 0.006 | 1.738 | |
pairwiseEMDDist | 0.418 | 0.004 | 0.422 | |