| Back to Multiple platform build/check report for BioC 3.18: simplified long |
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This page was generated on 2023-11-02 11:41:00 -0400 (Thu, 02 Nov 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.2 LTS) | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4729 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" | 4463 |
| lconway | macOS 12.6.5 Monterey | x86_64 | 4.3.1 Patched (2023-06-17 r84564) -- "Beagle Scouts" | 4478 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4464 |
| 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 1414/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| nipalsMCIA 1.0.0 (landing page) Maximilian Mattessich
| nebbiolo2 | Linux (Ubuntu 22.04.2 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.6.5 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.1 Ventura / arm64 | see weekly results here | ||||||||||||
| 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: 1.0.0 |
| Command: /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:nipalsMCIA.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings nipalsMCIA_1.0.0.tar.gz |
| StartedAt: 2023-11-02 12:41:49 -0000 (Thu, 02 Nov 2023) |
| EndedAt: 2023-11-02 12:50:01 -0000 (Thu, 02 Nov 2023) |
| EllapsedTime: 492.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: nipalsMCIA.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:nipalsMCIA.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings nipalsMCIA_1.0.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/nipalsMCIA.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (GCC) 10.3.1
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 ‘1.0.0’
* 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 R 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 21.287 0.072 21.403
block_weights_heatmap 17.940 0.763 19.305
ord_loadings 16.211 0.012 16.264
vis_load_ord 15.767 0.068 15.874
get_colors 15.540 0.060 15.633
global_scores_eigenvalues_plot 15.319 0.043 15.393
get_metadata_colors 15.211 0.036 15.278
projection_plot 14.691 0.032 14.757
vis_load_plot 14.317 0.036 14.383
nmb_get_bs 11.674 0.016 11.720
nmb_get_gs 10.816 0.076 10.915
nmb_get_bs_weights 9.893 0.983 12.601
nmb_get_eigs 10.763 0.076 10.866
nmb_get_metadata 10.665 0.008 10.696
nmb_get_gl 9.337 0.047 9.403
nmb_get_bl 9.345 0.032 9.399
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... 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-4.3.1/bin/R CMD INSTALL nipalsMCIA ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.3.1/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 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (64-bit)
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
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 52 ]
>
> proc.time()
user system elapsed
44.614 1.297 50.010
nipalsMCIA.Rcheck/nipalsMCIA-Ex.timings
| name | user | system | elapsed | |
| block_preproc | 0 | 0 | 0 | |
| block_weights_heatmap | 17.940 | 0.763 | 19.305 | |
| cc_preproc | 0 | 0 | 0 | |
| col_preproc | 0 | 0 | 0 | |
| deflate_block_bl | 0 | 0 | 0 | |
| deflate_block_gs | 0.001 | 0.000 | 0.000 | |
| extract_from_mae | 0.864 | 0.056 | 0.922 | |
| get_colors | 15.540 | 0.060 | 15.633 | |
| get_metadata_colors | 15.211 | 0.036 | 15.278 | |
| get_tv | 0.317 | 0.012 | 0.330 | |
| global_scores_eigenvalues_plot | 15.319 | 0.043 | 15.393 | |
| nipals_iter | 0.419 | 0.004 | 0.424 | |
| nipals_multiblock | 21.287 | 0.072 | 21.403 | |
| nmb_get_bl | 9.345 | 0.032 | 9.399 | |
| nmb_get_bs | 11.674 | 0.016 | 11.720 | |
| nmb_get_bs_weights | 9.893 | 0.983 | 12.601 | |
| nmb_get_eigs | 10.763 | 0.076 | 10.866 | |
| nmb_get_gl | 9.337 | 0.047 | 9.403 | |
| nmb_get_gs | 10.816 | 0.076 | 10.915 | |
| nmb_get_metadata | 10.665 | 0.008 | 10.696 | |
| ord_loadings | 16.211 | 0.012 | 16.264 | |
| predict_gs | 1.800 | 0.016 | 1.821 | |
| projection_plot | 14.691 | 0.032 | 14.757 | |
| simple_mae | 0.493 | 0.008 | 0.502 | |
| vis_load_ord | 15.767 | 0.068 | 15.874 | |
| vis_load_plot | 14.317 | 0.036 | 14.383 | |