| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-05-01 11:35:50 -0400 (Wed, 01 May 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" | 4753 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 beta (2024-04-14 r86421) -- "Puppy Cup" | 4518 |
| 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 497/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| CytoMDS 1.0.0 (landing page) Philippe Hauchamps
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | see weekly results here | ||||||||||||
|
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: 1.0.0 |
| Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:CytoMDS.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings CytoMDS_1.0.0.tar.gz |
| StartedAt: 2024-05-01 04:32:24 -0400 (Wed, 01 May 2024) |
| EndedAt: 2024-05-01 04:39:16 -0400 (Wed, 01 May 2024) |
| EllapsedTime: 411.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: CytoMDS.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:CytoMDS.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings CytoMDS_1.0.0.tar.gz
###
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##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/CytoMDS.Rcheck’
* using R version 4.4.0 beta (2024-04-15 r86425)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* 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 loading without being on the library search path ... 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 4.982 0.184 5.166
ggplotSampleMDSWrapBiplots 4.981 0.091 5.071
* 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: 1 NOTE
See
‘/home/biocbuild/bbs-3.19-bioc/meat/CytoMDS.Rcheck/00check.log’
for details.
CytoMDS.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL CytoMDS ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-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)
CytoMDS.Rcheck/tests/testthat.Rout
R version 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup"
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.
> # 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
70.451 2.636 169.959
CytoMDS.Rcheck/CytoMDS-Ex.timings
| name | user | system | elapsed | |
| EMDDist | 0.531 | 0.007 | 0.541 | |
| MDS | 2.092 | 0.141 | 2.234 | |
| channelSummaryStats | 2.189 | 0.084 | 2.274 | |
| computeMetricMDS | 2.587 | 0.028 | 2.615 | |
| ggplotMarginalDensities | 1.686 | 0.160 | 1.846 | |
| ggplotSampleMDS | 4.982 | 0.184 | 5.166 | |
| ggplotSampleMDSShepard | 2.590 | 0.084 | 2.673 | |
| ggplotSampleMDSWrapBiplots | 4.981 | 0.091 | 5.071 | |
| pairwiseEMDDist | 1.304 | 0.052 | 1.356 | |