| Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-12-23 12:06 -0500 (Mon, 23 Dec 2024).
| 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" | 4744 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
| 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 | | ||||||||
|
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: 2024-12-20 06:55:40 -0500 (Fri, 20 Dec 2024) |
| EndedAt: 2024-12-20 07:05:14 -0500 (Fri, 20 Dec 2024) |
| EllapsedTime: 573.5 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
###
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##############################################################################
* 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 13.200 0.426 13.824
block_weights_heatmap 12.684 0.533 13.541
vis_load_plot 11.422 0.311 12.142
get_colors 10.083 0.392 10.640
get_metadata_colors 9.962 0.326 10.435
ord_loadings 9.957 0.284 10.499
vis_load_ord 9.770 0.294 10.641
projection_plot 9.699 0.349 10.250
global_scores_eigenvalues_plot 9.174 0.337 9.607
nmb_get_gs 7.394 0.221 7.694
nmb_get_eigs 7.204 0.235 7.591
nmb_get_bs 7.156 0.243 7.515
nmb_get_metadata 6.766 0.203 7.046
nmb_get_bl 6.711 0.213 7.228
nmb_get_gl 6.671 0.186 6.928
nmb_get_bs_weights 6.610 0.231 7.059
* 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 9 | PASS 48 ]
══ Skipped tests (9) ═══════════════════════════════════════════════════════════
• empty test (9): 'test-block_weights_heatmap.R:5:1',
'test-global_scores_eigenvalues_plot.R:2:1',
'test-global_scores_heatmap.R:1:1', 'test-global_scores_heatmap.R:7:1',
'test-projection_plot.R:8:1', 'test-projection_plot.R:40:1',
'test-vis_load_ord.R:13:1', 'test-vis_load_plot.R:1:1',
'test-vis_load_plot.R:20:1'
[ FAIL 0 | WARN 0 | SKIP 9 | PASS 48 ]
>
> proc.time()
user system elapsed
71.085 2.014 77.455
nipalsMCIA.Rcheck/nipalsMCIA-Ex.timings
| name | user | system | elapsed | |
| block_preproc | 0.001 | 0.002 | 0.003 | |
| block_weights_heatmap | 12.684 | 0.533 | 13.541 | |
| cc_preproc | 0.001 | 0.000 | 0.001 | |
| col_preproc | 0.001 | 0.001 | 0.001 | |
| deflate_block_bl | 0.000 | 0.001 | 0.000 | |
| deflate_block_gs | 0.001 | 0.000 | 0.001 | |
| extract_from_mae | 1.528 | 0.055 | 1.609 | |
| get_colors | 10.083 | 0.392 | 10.640 | |
| get_metadata_colors | 9.962 | 0.326 | 10.435 | |
| get_tv | 0.509 | 0.007 | 0.519 | |
| global_scores_eigenvalues_plot | 9.174 | 0.337 | 9.607 | |
| nipals_iter | 0.543 | 0.008 | 0.555 | |
| nipals_multiblock | 13.200 | 0.426 | 13.824 | |
| nmb_get_bl | 6.711 | 0.213 | 7.228 | |
| nmb_get_bs | 7.156 | 0.243 | 7.515 | |
| nmb_get_bs_weights | 6.610 | 0.231 | 7.059 | |
| nmb_get_eigs | 7.204 | 0.235 | 7.591 | |
| nmb_get_gl | 6.671 | 0.186 | 6.928 | |
| nmb_get_gs | 7.394 | 0.221 | 7.694 | |
| nmb_get_metadata | 6.766 | 0.203 | 7.046 | |
| ord_loadings | 9.957 | 0.284 | 10.499 | |
| predict_gs | 2.343 | 0.040 | 2.409 | |
| projection_plot | 9.699 | 0.349 | 10.250 | |
| simple_mae | 0.826 | 0.007 | 0.876 | |
| vis_load_ord | 9.770 | 0.294 | 10.641 | |
| vis_load_plot | 11.422 | 0.311 | 12.142 | |