| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-10-13 11:39 -0400 (Mon, 13 Oct 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4833 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4614 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4555 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4586 |
| 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 1446/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| nipalsMCIA 1.6.0 (landing page) Maximilian Mattessich
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | 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 | | ||||||||
| kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | ERROR | skipped | ||||||||||
|
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: 1.6.0 |
| 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_1.6.0.tar.gz |
| StartedAt: 2025-10-10 07:31:06 -0400 (Fri, 10 Oct 2025) |
| EndedAt: 2025-10-10 07:40:59 -0400 (Fri, 10 Oct 2025) |
| EllapsedTime: 593.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: nipalsMCIA.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### 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_1.6.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/nipalsMCIA.Rcheck’
* using R version 4.5.1 RC (2025-06-05 r88288)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 14.2.0
* 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 ‘1.6.0’
* 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 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
block_weights_heatmap 12.931 0.548 13.581
nipals_multiblock 12.255 0.445 12.818
vis_load_plot 12.118 0.439 12.595
projection_plot 10.018 0.422 10.582
vis_load_ord 9.987 0.394 10.641
get_colors 9.952 0.368 10.610
global_scores_eigenvalues_plot 9.967 0.346 10.951
ord_loadings 9.323 0.382 9.832
get_metadata_colors 8.965 0.302 9.417
nmb_get_gs 7.469 0.274 8.043
nmb_get_bs_weights 7.447 0.269 7.827
nmb_get_bl 7.382 0.289 7.745
nmb_get_metadata 7.245 0.259 7.646
nmb_get_eigs 6.767 0.230 7.085
nmb_get_gl 6.738 0.196 7.024
nmb_get_bs 6.661 0.256 7.022
* 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/4.5-x86_64/Resources/library’ * installing *source* package ‘nipalsMCIA’ ... ** this is package ‘nipalsMCIA’ version ‘1.6.0’ ** 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 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root"
Copyright (C) 2025 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
|
| | 0%
|
|= | 2%
|
|== | 3%
|
|=== | 5%
|
|==== | 6%
|
|===== | 8%
|
|======= | 9%
|
|======== | 11%
|
|========= | 12%
|
|========== | 14%
|
|=========== | 16%
|
|============ | 17%
|
|============= | 19%
|
|============== | 20%
|
|=============== | 22%
|
|================ | 23%
|
|================== | 25%
|
|=================== | 27%
|
|==================== | 28%
|
|===================== | 30%
|
|====================== | 31%
|
|======================= | 33%
|
|======================== | 34%
|
|========================= | 36%
|
|========================== | 38%
|
|=========================== | 39%
|
|============================ | 41%
|
|============================== | 42%
|
|=============================== | 44%
|
|================================ | 45%
|
|================================= | 47%
|
|================================== | 48%
|
|=================================== | 50%
|
|==================================== | 52%
|
|===================================== | 53%
|
|====================================== | 55%
|
|======================================= | 56%
|
|======================================== | 58%
|
|========================================== | 59%
|
|=========================================== | 61%
|
|============================================ | 62%
|
|============================================= | 64%
|
|============================================== | 66%
|
|=============================================== | 67%
|
|================================================ | 69%
|
|================================================= | 70%
|
|================================================== | 72%
|
|=================================================== | 73%
|
|==================================================== | 75%
|
|====================================================== | 77%
|
|======================================================= | 78%
|
|======================================================== | 80%
|
|========================================================= | 81%
|
|========================================================== | 83%
|
|=========================================================== | 84%
|
|============================================================ | 86%
|
|============================================================= | 88%
|
|============================================================== | 89%
|
|=============================================================== | 91%
|
|================================================================= | 92%
|
|================================================================== | 94%
|
|=================================================================== | 95%
|
|==================================================================== | 97%
|
|===================================================================== | 98%
|
|======================================================================| 100%
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
75.394 1.997 81.632
nipalsMCIA.Rcheck/nipalsMCIA-Ex.timings
| name | user | system | elapsed | |
| block_preproc | 0.001 | 0.001 | 0.002 | |
| block_weights_heatmap | 12.931 | 0.548 | 13.581 | |
| cc_preproc | 0.000 | 0.001 | 0.001 | |
| col_preproc | 0.001 | 0.000 | 0.001 | |
| deflate_block_bl | 0.000 | 0.000 | 0.001 | |
| deflate_block_gs | 0.001 | 0.001 | 0.001 | |
| extract_from_mae | 1.554 | 0.112 | 1.684 | |
| get_colors | 9.952 | 0.368 | 10.610 | |
| get_metadata_colors | 8.965 | 0.302 | 9.417 | |
| get_tv | 0.476 | 0.010 | 0.489 | |
| global_scores_eigenvalues_plot | 9.967 | 0.346 | 10.951 | |
| nipals_iter | 0.504 | 0.013 | 0.578 | |
| nipals_multiblock | 12.255 | 0.445 | 12.818 | |
| nmb_get_bl | 7.382 | 0.289 | 7.745 | |
| nmb_get_bs | 6.661 | 0.256 | 7.022 | |
| nmb_get_bs_weights | 7.447 | 0.269 | 7.827 | |
| nmb_get_eigs | 6.767 | 0.230 | 7.085 | |
| nmb_get_gl | 6.738 | 0.196 | 7.024 | |
| nmb_get_gs | 7.469 | 0.274 | 8.043 | |
| nmb_get_metadata | 7.245 | 0.259 | 7.646 | |
| ord_loadings | 9.323 | 0.382 | 9.832 | |
| predict_gs | 2.312 | 0.041 | 2.372 | |
| projection_plot | 10.018 | 0.422 | 10.582 | |
| simple_mae | 0.808 | 0.010 | 0.836 | |
| vis_load_ord | 9.987 | 0.394 | 10.641 | |
| vis_load_plot | 12.118 | 0.439 | 12.595 | |