| Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-11-20 12:07 -0500 (Wed, 20 Nov 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4481 |
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4479 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4359 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4539 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4493 |
| 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 1.4.0 (landing page) Maximilian Mattessich
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | ||||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / 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: 1.4.0 |
| 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_1.4.0.tar.gz |
| StartedAt: 2024-11-20 10:30:46 -0000 (Wed, 20 Nov 2024) |
| EndedAt: 2024-11-20 10:38:54 -0000 (Wed, 20 Nov 2024) |
| EllapsedTime: 487.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: nipalsMCIA.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### 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_1.4.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/nipalsMCIA.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14)
GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘nipalsMCIA/DESCRIPTION’ ... OK
* this is package ‘nipalsMCIA’ version ‘1.4.0’
* 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 17.345 0.124 17.240
ord_loadings 16.791 0.096 16.923
vis_load_plot 16.042 0.071 16.149
block_weights_heatmap 15.780 0.187 16.002
vis_load_ord 15.862 0.068 15.963
projection_plot 15.868 0.016 15.832
get_colors 13.703 0.148 13.880
get_metadata_colors 13.688 0.048 13.765
global_scores_eigenvalues_plot 13.114 0.028 13.169
nmb_get_eigs 11.398 0.116 11.539
nmb_get_metadata 11.033 0.020 11.076
nmb_get_bs 10.742 0.039 10.805
nmb_get_gs 10.636 0.076 10.733
nmb_get_bs_weights 10.175 0.019 10.217
nmb_get_gl 10.025 0.020 10.067
nmb_get_bl 9.690 0.004 9.713
* 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-4.4.1/site-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 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 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
45.167 1.363 50.424
nipalsMCIA.Rcheck/nipalsMCIA-Ex.timings
| name | user | system | elapsed | |
| block_preproc | 0.000 | 0.000 | 0.001 | |
| block_weights_heatmap | 15.780 | 0.187 | 16.002 | |
| cc_preproc | 0.001 | 0.000 | 0.000 | |
| col_preproc | 0 | 0 | 0 | |
| deflate_block_bl | 0.000 | 0.000 | 0.001 | |
| deflate_block_gs | 0.000 | 0.000 | 0.001 | |
| extract_from_mae | 0.913 | 0.016 | 0.931 | |
| get_colors | 13.703 | 0.148 | 13.880 | |
| get_metadata_colors | 13.688 | 0.048 | 13.765 | |
| get_tv | 0.328 | 0.008 | 0.337 | |
| global_scores_eigenvalues_plot | 13.114 | 0.028 | 13.169 | |
| nipals_iter | 0.343 | 0.008 | 0.351 | |
| nipals_multiblock | 17.345 | 0.124 | 17.240 | |
| nmb_get_bl | 9.690 | 0.004 | 9.713 | |
| nmb_get_bs | 10.742 | 0.039 | 10.805 | |
| nmb_get_bs_weights | 10.175 | 0.019 | 10.217 | |
| nmb_get_eigs | 11.398 | 0.116 | 11.539 | |
| nmb_get_gl | 10.025 | 0.020 | 10.067 | |
| nmb_get_gs | 10.636 | 0.076 | 10.733 | |
| nmb_get_metadata | 11.033 | 0.020 | 11.076 | |
| ord_loadings | 16.791 | 0.096 | 16.923 | |
| predict_gs | 1.683 | 0.020 | 1.707 | |
| projection_plot | 15.868 | 0.016 | 15.832 | |
| simple_mae | 0.496 | 0.000 | 0.496 | |
| vis_load_ord | 15.862 | 0.068 | 15.963 | |
| vis_load_plot | 16.042 | 0.071 | 16.149 | |