| Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2025-01-23 12:09 -0500 (Thu, 23 Jan 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4746 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4493 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4517 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4469 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4394 |
| 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 1418/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| nipalsMCIA 1.4.2 (landing page) Maximilian Mattessich
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
|
To the developers/maintainers of the nipalsMCIA package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/nipalsMCIA.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: nipalsMCIA |
| Version: 1.4.2 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:nipalsMCIA.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings nipalsMCIA_1.4.2.tar.gz |
| StartedAt: 2025-01-21 07:30:44 -0500 (Tue, 21 Jan 2025) |
| EndedAt: 2025-01-21 07:40:28 -0500 (Tue, 21 Jan 2025) |
| EllapsedTime: 583.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: nipalsMCIA.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:nipalsMCIA.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings nipalsMCIA_1.4.2.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/nipalsMCIA.Rcheck’
* using R version 4.4.2 (2024-10-31)
* 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 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘nipalsMCIA/DESCRIPTION’ ... OK
* this is package ‘nipalsMCIA’ version ‘1.4.2’
* 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 ‘nipalsMCIA’ 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 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... 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
nipals_multiblock 13.088 0.371 14.081
block_weights_heatmap 12.781 0.549 13.801
vis_load_plot 10.869 0.334 11.938
vis_load_ord 10.383 0.348 11.383
get_colors 10.192 0.329 10.988
ord_loadings 10.149 0.270 10.971
get_metadata_colors 9.961 0.284 10.695
global_scores_eigenvalues_plot 9.406 0.246 10.095
projection_plot 9.258 0.287 9.896
nmb_get_gs 7.389 0.213 7.953
nmb_get_eigs 7.302 0.219 7.851
nmb_get_bs 7.221 0.230 8.020
nmb_get_metadata 6.757 0.193 7.155
nmb_get_bs_weights 6.682 0.204 7.445
nmb_get_bl 6.704 0.178 7.120
nmb_get_gl 6.650 0.212 6.970
* 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: OK
nipalsMCIA.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL nipalsMCIA ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * installing *source* package ‘nipalsMCIA’ ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** 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 (nipalsMCIA)
nipalsMCIA.Rcheck/tests/testthat.Rout
R version 4.4.2 (2024-10-31) -- "Pile of Leaves"
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.
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
>
> library(nipalsMCIA)
> library(testthat)
>
> test_check("nipalsMCIA")
Performing column-level pre-processing...
Column pre-processing completed.
Performing block-level preprocessing...
Block pre-processing completed.
Computing order 1 scores
Computing order 2 scores
Performing column-level pre-processing...
Column pre-processing completed.
Performing block-level preprocessing...
Block pre-processing completed.
Computing order 1 scores
Computing order 2 scores
Computing order 3 scores
Performing column-level pre-processing...
Column pre-processing completed.
Performing block-level preprocessing...
Block pre-processing completed.
Computing order 1 scores
Computing order 2 scores
Running GSEA for Factor 1
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Performing column-level pre-processing...
Column pre-processing completed.
Performing block-level preprocessing...
Block pre-processing completed.
Computing order 1 scores
Computing order 2 scores
Computing order 3 scores
Computing order 4 scores
Performing pre-processing on data
Pre-processing completed
color_col option not recognized, defaulting to black/white plotting.
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 57 ]
>
> proc.time()
user system elapsed
70.961 2.107 78.272
nipalsMCIA.Rcheck/nipalsMCIA-Ex.timings
| name | user | system | elapsed | |
| block_preproc | 0.001 | 0.001 | 0.003 | |
| block_weights_heatmap | 12.781 | 0.549 | 13.801 | |
| cc_preproc | 0.000 | 0.000 | 0.003 | |
| col_preproc | 0.001 | 0.000 | 0.000 | |
| deflate_block_bl | 0.000 | 0.000 | 0.001 | |
| deflate_block_gs | 0.001 | 0.001 | 0.001 | |
| extract_from_mae | 1.621 | 0.077 | 1.875 | |
| get_colors | 10.192 | 0.329 | 10.988 | |
| get_metadata_colors | 9.961 | 0.284 | 10.695 | |
| get_tv | 0.524 | 0.007 | 0.564 | |
| global_scores_eigenvalues_plot | 9.406 | 0.246 | 10.095 | |
| nipals_iter | 0.546 | 0.007 | 0.582 | |
| nipals_multiblock | 13.088 | 0.371 | 14.081 | |
| nmb_get_bl | 6.704 | 0.178 | 7.120 | |
| nmb_get_bs | 7.221 | 0.230 | 8.020 | |
| nmb_get_bs_weights | 6.682 | 0.204 | 7.445 | |
| nmb_get_eigs | 7.302 | 0.219 | 7.851 | |
| nmb_get_gl | 6.650 | 0.212 | 6.970 | |
| nmb_get_gs | 7.389 | 0.213 | 7.953 | |
| nmb_get_metadata | 6.757 | 0.193 | 7.155 | |
| ord_loadings | 10.149 | 0.270 | 10.971 | |
| predict_gs | 2.378 | 0.033 | 2.499 | |
| projection_plot | 9.258 | 0.287 | 9.896 | |
| simple_mae | 0.855 | 0.007 | 0.946 | |
| vis_load_ord | 10.383 | 0.348 | 11.383 | |
| vis_load_plot | 10.869 | 0.334 | 11.938 | |