| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-11-12 11:58 -0500 (Wed, 12 Nov 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4902 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4668 |
| 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 1463/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| nipalsMCIA 1.8.0 (landing page) Maximilian Mattessich
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | 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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: nipalsMCIA |
| Version: 1.8.0 |
| Command: /home/biocbuild/R/R/bin/R CMD check --install=check:nipalsMCIA.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings nipalsMCIA_1.8.0.tar.gz |
| StartedAt: 2025-11-11 12:30:19 -0000 (Tue, 11 Nov 2025) |
| EndedAt: 2025-11-11 12:37:04 -0000 (Tue, 11 Nov 2025) |
| EllapsedTime: 405.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: nipalsMCIA.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### /home/biocbuild/R/R/bin/R CMD check --install=check:nipalsMCIA.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings nipalsMCIA_1.8.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/nipalsMCIA.Rcheck’
* using R version 4.5.0 (2025-04-11)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘nipalsMCIA/DESCRIPTION’ ... OK
* this is package ‘nipalsMCIA’ version ‘1.8.0’
* 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 ‘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 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 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 11.688 0.127 11.940
block_weights_heatmap 10.368 0.243 10.687
vis_load_ord 8.946 0.023 8.994
ord_loadings 8.840 0.008 8.871
vis_load_plot 8.787 0.012 8.926
get_colors 8.406 0.152 8.661
get_metadata_colors 7.760 0.223 8.006
global_scores_eigenvalues_plot 7.729 0.048 7.849
projection_plot 7.741 0.008 7.833
nmb_get_bs 6.903 0.124 7.047
nmb_get_metadata 6.202 0.008 6.225
nmb_get_bl 5.957 0.068 6.055
nmb_get_eigs 5.996 0.016 6.029
nmb_get_bs_weights 5.608 0.012 5.743
nmb_get_gs 5.457 0.016 5.487
nmb_get_gl 5.129 0.012 5.155
* 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: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL nipalsMCIA ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’ * installing *source* package ‘nipalsMCIA’ ... ** this is package ‘nipalsMCIA’ version ‘1.8.0’ ** 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 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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.
> # 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
44.419 1.015 55.039
nipalsMCIA.Rcheck/nipalsMCIA-Ex.timings
| name | user | system | elapsed | |
| block_preproc | 0.000 | 0.000 | 0.001 | |
| block_weights_heatmap | 10.368 | 0.243 | 10.687 | |
| cc_preproc | 0.000 | 0.000 | 0.001 | |
| col_preproc | 0.000 | 0.000 | 0.001 | |
| deflate_block_bl | 0 | 0 | 0 | |
| deflate_block_gs | 0.001 | 0.000 | 0.000 | |
| extract_from_mae | 0.866 | 0.056 | 0.923 | |
| get_colors | 8.406 | 0.152 | 8.661 | |
| get_metadata_colors | 7.760 | 0.223 | 8.006 | |
| get_tv | 0.300 | 0.004 | 0.304 | |
| global_scores_eigenvalues_plot | 7.729 | 0.048 | 7.849 | |
| nipals_iter | 0.303 | 0.016 | 0.321 | |
| nipals_multiblock | 11.688 | 0.127 | 11.940 | |
| nmb_get_bl | 5.957 | 0.068 | 6.055 | |
| nmb_get_bs | 6.903 | 0.124 | 7.047 | |
| nmb_get_bs_weights | 5.608 | 0.012 | 5.743 | |
| nmb_get_eigs | 5.996 | 0.016 | 6.029 | |
| nmb_get_gl | 5.129 | 0.012 | 5.155 | |
| nmb_get_gs | 5.457 | 0.016 | 5.487 | |
| nmb_get_metadata | 6.202 | 0.008 | 6.225 | |
| ord_loadings | 8.840 | 0.008 | 8.871 | |
| predict_gs | 1.441 | 0.000 | 1.480 | |
| projection_plot | 7.741 | 0.008 | 7.833 | |
| simple_mae | 0.450 | 0.000 | 0.451 | |
| vis_load_ord | 8.946 | 0.023 | 8.994 | |
| vis_load_plot | 8.787 | 0.012 | 8.926 | |