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This page was generated on 2024-12-23 12:07 -0500 (Mon, 23 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4744
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4487
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4515
kjohnson1macOS 13.6.6 Venturaarm644.4.2 (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 1418/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
nipalsMCIA 1.4.2  (landing page)
Maximilian Mattessich
Snapshot Date: 2024-12-19 13:00 -0500 (Thu, 19 Dec 2024)
git_url: https://git.bioconductor.org/packages/nipalsMCIA
git_branch: RELEASE_3_20
git_last_commit: 6bee2e9
git_last_commit_date: 2024-12-18 11:42:53 -0500 (Wed, 18 Dec 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  YES
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  YES
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  YES
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  YES


CHECK results for nipalsMCIA on kjohnson1

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.

raw results


Summary

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: 2024-12-21 03:17:05 -0500 (Sat, 21 Dec 2024)
EndedAt: 2024-12-21 03:22:32 -0500 (Sat, 21 Dec 2024)
EllapsedTime: 327.1 seconds
RetCode: 0
Status:   OK  
CheckDir: nipalsMCIA.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/nipalsMCIA.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: aarch64-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 Ventura 13.7.1
* 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
block_weights_heatmap          7.705  0.475   8.198
nipals_multiblock              7.011  0.556   7.584
vis_load_plot                  6.919  0.298   7.218
get_colors                     6.456  0.503   6.961
ord_loadings                   6.223  0.479   6.726
get_metadata_colors            6.216  0.444   6.697
projection_plot                5.994  0.394   6.389
global_scores_eigenvalues_plot 5.528  0.426   5.957
vis_load_ord                   5.656  0.167   5.824
nmb_get_bs                     4.723  0.399   5.126
nmb_get_eigs                   4.758  0.297   5.056
* 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


Installation output

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-arm64/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)

Tests output

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: aarch64-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 
 40.069   1.310  43.204 

Example timings

nipalsMCIA.Rcheck/nipalsMCIA-Ex.timings

nameusersystemelapsed
block_preproc0.0010.0010.002
block_weights_heatmap7.7050.4758.198
cc_preproc0.0010.0000.001
col_preproc0.0000.0010.001
deflate_block_bl0.0000.0000.001
deflate_block_gs0.0010.0000.001
extract_from_mae0.6680.0200.689
get_colors6.4560.5036.961
get_metadata_colors6.2160.4446.697
get_tv0.2880.0060.294
global_scores_eigenvalues_plot5.5280.4265.957
nipals_iter0.3070.0060.313
nipals_multiblock7.0110.5567.584
nmb_get_bl3.9170.3474.265
nmb_get_bs4.7230.3995.126
nmb_get_bs_weights3.8750.3384.213
nmb_get_eigs4.7580.2975.056
nmb_get_gl3.8600.2374.097
nmb_get_gs4.5640.1804.747
nmb_get_metadata3.8390.1624.000
ord_loadings6.2230.4796.726
predict_gs1.1070.0461.153
projection_plot5.9940.3946.389
simple_mae0.4030.0080.411
vis_load_ord5.6560.1675.824
vis_load_plot6.9190.2987.218