Back to Multiple platform build/check report for BioC 3.19:   simplified   long
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This page was generated on 2024-07-16 17:40 -0400 (Tue, 16 Jul 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4742
palomino7Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4484
merida1macOS 12.7.4 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4513
kjohnson1macOS 13.6.6 Venturaarm644.4.1 (2024-06-14) -- "Race for Your Life" 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 497/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CytoMDS 1.0.0  (landing page)
Philippe Hauchamps
Snapshot Date: 2024-07-14 14:00 -0400 (Sun, 14 Jul 2024)
git_url: https://git.bioconductor.org/packages/CytoMDS
git_branch: RELEASE_3_19
git_last_commit: 66cea35
git_last_commit_date: 2024-04-30 11:55:13 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  
merida1macOS 12.7.4 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for CytoMDS on merida1

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.

raw results


Summary

Package: CytoMDS
Version: 1.0.0
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_1.0.0.tar.gz
StartedAt: 2024-07-15 02:56:57 -0400 (Mon, 15 Jul 2024)
EndedAt: 2024-07-15 03:07:33 -0400 (Mon, 15 Jul 2024)
EllapsedTime: 636.6 seconds
RetCode: 0
Status:   OK  
CheckDir: CytoMDS.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/CytoMDS.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-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 Monterey 12.7.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CytoMDS/DESCRIPTION’ ... OK
* this is package ‘CytoMDS’ version ‘1.0.0’
* 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 ‘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
Examples with CPU (user + system) or elapsed time > 5s
                            user system elapsed
ggplotSampleMDS            6.317  0.096   8.156
ggplotSampleMDSWrapBiplots 6.269  0.064   7.790
MDS                        4.408  0.357   6.054
* 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-3.19-bioc/meat/CytoMDS.Rcheck/00check.log’
for details.


Installation output

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-x86_64/Resources/library’
* installing *source* package ‘CytoMDS’ ...
** using staged installation
** R
** 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)

Tests output

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: x86_64-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")

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[ FAIL 0 | WARN 0 | SKIP 4 | PASS 211 ]

══ Skipped tests (4) ═══════════════════════════════════════════════════════════
• On CRAN (4): 'test-ggplots.R:64:5', 'test-ggplots.R:181:5',
  'test-ggplots.R:544:5', 'test-ggplots.R:604:5'

[ FAIL 0 | WARN 0 | SKIP 4 | PASS 211 ]
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/ggplotsamplemdswrapbiplots-default-rows-and-cols-subset.svg
• ggplots/ggplotsamplemdswrapbiplots-no-legend.svg
• ggplots/ggplotsamplemdswrapbiplots-with-1-col.svg
• ggplots/ggplotsampmds-with-bipl-flpx-y.svg
> 
> proc.time()
   user  system elapsed 
102.320   2.713 370.465 

Example timings

CytoMDS.Rcheck/CytoMDS-Ex.timings

nameusersystemelapsed
EMDDist1.2810.0581.685
MDS4.4080.3576.054
channelSummaryStats3.1760.0433.916
computeMetricMDS3.5620.0464.470
ggplotMarginalDensities2.4630.1033.307
ggplotSampleMDS6.3170.0968.156
ggplotSampleMDSShepard3.6320.0454.659
ggplotSampleMDSWrapBiplots6.2690.0647.790
pairwiseEMDDist1.8010.0212.236