Back to Multiple platform build/check report for BioC 3.20:   simplified   long
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This page was generated on 2024-05-15 13:46:39 -0400 (Wed, 15 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" 4663
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4480
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 1540/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
POMA 1.15.0  (landing page)
Pol Castellano-Escuder
Snapshot Date: 2024-05-13 14:05:07 -0400 (Mon, 13 May 2024)
git_url: https://git.bioconductor.org/packages/POMA
git_branch: devel
git_last_commit: 7623cc5
git_last_commit_date: 2024-04-30 11:25:46 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  
kjohnson1macOS 13.6.6 Ventura / arm64see weekly results here

CHECK results for POMA on kunpeng2


To the developers/maintainers of the POMA package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/POMA.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.

raw results


Summary

Package: POMA
Version: 1.14.0
Command: /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:POMA.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings POMA_1.14.0.tar.gz
StartedAt: 2024-05-09 10:38:55 -0000 (Thu, 09 May 2024)
EndedAt: 2024-05-09 10:44:04 -0000 (Thu, 09 May 2024)
EllapsedTime: 308.6 seconds
RetCode: 0
Status:   OK  
CheckDir: POMA.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:POMA.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings POMA_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/POMA.Rcheck’
* using R version 4.4.0 beta (2024-04-15 r86425)
* using platform: aarch64-unknown-linux-gnu
* 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 ‘POMA/DESCRIPTION’ ... OK
* this is package ‘POMA’ version ‘1.14.0’
* 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 ‘POMA’ 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 whether startup messages can be suppressed ... OK
* checking dependencies in R code ... NOTE
Unexported object imported by a ':::' call: ‘utils:::.getHelpFile’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
PomaBatch: no visible global function definition for ‘is’
PomaBatch: no visible global function definition for ‘validObject’
PomaBoxplots: no visible global function definition for ‘is’
PomaBoxplots: no visible binding for global variable ‘sample_id’
PomaBoxplots: no visible binding for global variable ‘group_factor’
PomaBoxplots: no visible global function definition for ‘median’
PomaBoxplots: no visible binding for global variable ‘value’
PomaBoxplots: no visible global function definition for ‘reorder’
PomaBoxplots: no visible binding for global variable ‘median_rank’
PomaBoxplots: no visible binding for global variable ‘name’
PomaClust: no visible global function definition for ‘is’
PomaClust: no visible binding for global variable ‘clust’
PomaClust: no visible binding for global variable ‘V1’
PomaClust: no visible binding for global variable ‘V2’
PomaClust: no visible binding for global variable ‘Dim1’
PomaClust: no visible binding for global variable ‘Dim2’
PomaCorr: no visible global function definition for ‘is’
PomaCorr: no visible global function definition for ‘cor’
PomaCorr: no visible binding for global variable ‘column’
PomaCorr: no visible binding for global variable ‘cor’
PomaCorr: no visible binding for global variable ‘p’
PomaCorr: no visible global function definition for ‘p.adjust’
PomaCorr: no visible binding for global variable ‘pvalue’
PomaCorr: no visible binding for global variable ‘corr’
PomaCorr: no visible binding for global variable ‘feature1’
PomaCorr: no visible binding for global variable ‘name’
PomaCorr: no visible binding for global variable ‘value’
PomaCreateObject: no visible global function definition for
  ‘validObject’
PomaDESeq: no visible global function definition for ‘is’
PomaDESeq: no visible binding for global variable ‘padj’
PomaDESeq: no visible binding for global variable ‘adj_pvalue’
PomaDensity: no visible global function definition for ‘is’
PomaDensity: no visible binding for global variable ‘sample_id’
PomaDensity: no visible binding for global variable ‘group_factor’
PomaDensity: no visible binding for global variable ‘name’
PomaDensity: no visible binding for global variable ‘value’
PomaHeatmap: no visible global function definition for ‘is’
PomaImpute: no visible global function definition for ‘is’
PomaImpute: no visible global function definition for ‘aggregate’
PomaImpute: no visible binding for global variable ‘group_factor’
PomaImpute: no visible global function definition for ‘validObject’
PomaLM: no visible global function definition for ‘is’
PomaLM: no visible global function definition for ‘lm’
PomaLM: no visible global function definition for ‘p.adjust’
PomaLM: no visible binding for global variable ‘p.value’
PomaLM: no visible binding for global variable ‘term’
PomaLM: no visible binding for global variable ‘estimate’
PomaLM: no visible binding for global variable ‘std.error’
PomaLM: no visible binding for global variable ‘statistic’
PomaLM: no visible binding for global variable ‘adj_pvalue’
PomaLM: no visible binding for global variable ‘pvalue’
PomaLM: no visible global function definition for ‘reorder’
PomaLM: no visible binding for global variable ‘feature’
PomaLM: no visible binding for global variable ‘std_err’
PomaLMM: no visible global function definition for ‘is’
PomaLMM : lmm_fun: no visible global function definition for ‘vcov’
PomaLMM : lmm_fun: no visible binding for global variable ‘vcov’
PomaLMM : lmm_fun: no visible binding for global variable ‘grp’
PomaLMM : lmm_fun: no visible binding for global variable
  ‘variance_percent’
PomaLMM: no visible binding for global variable ‘feature’
PomaLMM: no visible binding for global variable ‘name’
PomaLMM: no visible binding for global variable ‘value’
PomaLasso: no visible global function definition for ‘is’
PomaLasso: no visible binding for global variable ‘estimate’
PomaLasso: no visible binding for global variable ‘conf.low’
PomaLasso: no visible binding for global variable ‘conf.high’
PomaLasso: no visible global function definition for ‘predict’
PomaLasso: no visible binding for global variable ‘term’
PomaLimma: no visible global function definition for ‘is’
PomaLimma: no visible global function definition for ‘as.formula’
PomaLimma: no visible binding for global variable ‘P.Value’
PomaLimma: no visible binding for global variable ‘adj.P.Val’
PomaNorm: no visible global function definition for ‘is’
PomaNorm: no visible binding for global variable ‘var’
PomaNorm : <anonymous>: no visible global function definition for ‘sd’
PomaNorm: no visible global function definition for ‘validObject’
PomaOddsRatio: no visible global function definition for ‘is’
PomaOddsRatio: no visible binding for global variable ‘group’
PomaOddsRatio: no visible binding for global variable ‘OddsRatio’
PomaOddsRatio: no visible binding for global variable ‘feature’
PomaOddsRatio: no visible binding for global variable ‘upr’
PomaOddsRatio: no visible binding for global variable ‘lwr’
PomaOutliers: no visible global function definition for ‘is’
PomaOutliers: no visible binding for global variable ‘groups’
PomaOutliers: no visible global function definition for ‘quantile’
PomaOutliers: no visible global function definition for ‘IQR’
PomaOutliers: no visible binding for global variable ‘limit’
PomaOutliers: no visible binding for global variable ‘out’
PomaOutliers : find_hull: no visible global function definition for
  ‘chull’
PomaOutliers: no visible binding for global variable ‘group’
PomaOutliers: no visible binding for global variable ‘.’
PomaOutliers: no visible binding for global variable ‘PCoA1’
PomaOutliers: no visible binding for global variable ‘PCoA2’
PomaOutliers: no visible global function definition for ‘validObject’
PomaPCA: no visible global function definition for ‘is’
PomaPCA: no visible global function definition for ‘prcomp’
PomaPCA: no visible binding for global variable ‘PC1’
PomaPCA: no visible binding for global variable ‘PC2’
PomaPCA: no visible binding for global variable ‘group’
PomaPCA: no visible binding for global variable ‘sample_id’
PomaPCA: no visible global function definition for ‘reorder’
PomaPCA: no visible binding for global variable ‘comp’
PomaPCA: no visible binding for global variable ‘var_exp’
PomaPCA: no visible binding for global variable ‘feature’
PomaPCA: no visible binding for global variable ‘value’
PomaPCA: no visible binding for global variable ‘name’
PomaPCA: no visible binding for global variable ‘to_x’
PomaPCA: no visible binding for global variable ‘to_y’
PomaPCR: no visible global function definition for ‘is’
PomaPCR: no visible binding for global variable ‘PC1’
PomaPCR: no visible global function definition for ‘lm’
PomaPCR: no visible global function definition for ‘p.adjust’
PomaPCR: no visible binding for global variable ‘p.value’
PomaPCR: no visible binding for global variable ‘term’
PomaPCR: no visible binding for global variable ‘estimate’
PomaPCR: no visible binding for global variable ‘std.error’
PomaPCR: no visible binding for global variable ‘statistic’
PomaPCR: no visible binding for global variable ‘adj_pvalue’
PomaPCR: no visible binding for global variable ‘pvalue’
PomaPLS: no visible global function definition for ‘is’
PomaPLS: no visible binding for global variable ‘comp1’
PomaPLS: no visible binding for global variable ‘comp2’
PomaPLS: no visible binding for global variable ‘sample_id’
PomaPLS: no visible binding for global variable ‘feature’
PomaPLS: no visible global function definition for ‘reorder’
PomaPLS: no visible binding for global variable ‘value’
PomaPLS: no visible binding for global variable ‘name’
PomaPLS: no visible binding for global variable ‘component’
PomaPLS: no visible binding for global variable ‘error’
PomaPLS: no visible binding for global variable ‘feature_sd’
PomaPLS: no visible binding for global variable ‘sd’
PomaRandForest: no visible global function definition for ‘is’
PomaRandForest: no visible binding for global variable ‘OOB’
PomaRandForest: no visible binding for global variable
  ‘MeanDecreaseGini’
PomaRandForest: no visible global function definition for ‘reorder’
PomaRandForest: no visible binding for global variable ‘feature’
PomaRankProd: no visible global function definition for ‘is’
PomaRankProd: no visible binding for global variable ‘P.value’
PomaRankProd: no visible binding for global variable ‘gene.index’
PomaUMAP: no visible global function definition for ‘is’
PomaUMAP: no visible binding for global variable ‘clust’
PomaUMAP: no visible binding for global variable ‘UMAP1’
PomaUMAP: no visible binding for global variable ‘UMAP2’
PomaUnivariate: no visible global function definition for ‘is’
PomaUnivariate: no visible binding for global variable ‘group’
PomaUnivariate : <anonymous>: no visible global function definition for
  ‘t.test’
PomaUnivariate: no visible global function definition for ‘p.adjust’
PomaUnivariate: no visible binding for global variable ‘pvalue’
PomaUnivariate: no visible binding for global variable ‘feature’
PomaUnivariate: no visible binding for global variable ‘fold_change’
PomaUnivariate: no visible binding for global variable ‘diff_means’
PomaUnivariate: no visible binding for global variable ‘adj_pvalue’
PomaUnivariate : <anonymous>: no visible global function definition for
  ‘anova’
PomaUnivariate : <anonymous>: no visible global function definition for
  ‘aov’
PomaUnivariate: no visible global function definition for ‘TukeyHSD’
PomaUnivariate: no visible global function definition for ‘aov’
PomaUnivariate: no visible binding for global variable ‘adj.p.value’
PomaUnivariate: no visible global function definition for ‘as.formula’
PomaUnivariate: no visible binding for global variable ‘term’
PomaUnivariate: no visible binding for global variable ‘p.value’
PomaUnivariate: no visible binding for global variable ‘contrast’
PomaUnivariate: no visible binding for global variable ‘p adj’
PomaUnivariate : <anonymous>: no visible global function definition for
  ‘wilcox.test’
PomaUnivariate : <anonymous>: no visible global function definition for
  ‘kruskal.test’
PomaUnivariate: no visible binding for global variable ‘kw_rank_sum’
PomaUnivariate: no visible binding for global variable ‘Comparison’
PomaUnivariate: no visible binding for global variable ‘P.adj’
PomaVolcano: no visible global function definition for ‘quantile’
PomaVolcano: no visible binding for global variable ‘logFC’
PomaVolcano: no visible binding for global variable ‘pvalue’
PomaVolcano: no visible binding for global variable ‘feature’
create_mock_data: no visible global function definition for ‘runif’
create_mock_summarized_experiment: no visible global function
  definition for ‘runif’
help_extract: no visible global function definition for
  ‘capture.output’
make_legend: no visible binding for global variable ‘POMA’
title_extract: no visible global function definition for
  ‘capture.output’
Undefined global functions or variables:
  . Comparison Dim1 Dim2 IQR MeanDecreaseGini OOB OddsRatio P.Value
  P.adj P.value PC1 PC2 PCoA1 PCoA2 POMA TukeyHSD UMAP1 UMAP2 V1 V2
  adj.P.Val adj.p.value adj_pvalue aggregate anova aov as.formula
  capture.output chull clust column comp comp1 comp2 component
  conf.high conf.low contrast cor corr diff_means error estimate
  feature feature1 feature_sd fold_change gene.index group group_factor
  groups grp is kruskal.test kw_rank_sum limit lm logFC lwr median
  median_rank name out p p adj p.adjust p.value padj prcomp predict
  pvalue quantile reorder runif sample_id sd statistic std.error
  std_err t.test term to_x to_y upr validObject value var var_exp
  variance_percent vcov wilcox.test
Consider adding
  importFrom("grDevices", "chull")
  importFrom("methods", "is", "validObject")
  importFrom("stats", "IQR", "TukeyHSD", "aggregate", "anova", "aov",
             "as.formula", "cor", "kruskal.test", "lm", "median",
             "p.adjust", "prcomp", "predict", "quantile", "reorder",
             "runif", "sd", "t.test", "var", "vcov", "wilcox.test")
  importFrom("utils", "capture.output")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 LazyData ... 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
PomaUnivariate 63.757  0.563  64.455
PomaPLS        22.628  1.124  23.804
PomaBoxplots   23.008  0.527  23.586
PomaLMM        19.269  0.367  19.692
PomaBatch      15.760  0.958  16.755
PomaHeatmap     9.337  0.431   9.794
PomaUMAP        4.859  0.192   5.068
* 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/POMA.Rcheck/00check.log’
for details.


Installation output

POMA.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD INSTALL POMA
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library’
* installing *source* package ‘POMA’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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 (POMA)

Tests output

POMA.Rcheck/tests/testthat.Rout


R version 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup"
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.

> library(testthat)
> library(POMA)
Welcome to POMA!
Version 1.14.0
POMAShiny app: https://github.com/pcastellanoescuder/POMAShiny
> 
> test_check("POMA")
Rank Product analysis for unpaired case 
 

 done  No genes called significant under class1 < class2 

No genes called significant under class1 > class2 

Rank Product analysis for unpaired case 
 

 done  No genes called significant under class1 < class2 

No genes called significant under class1 > class2 

Rank Product analysis for unpaired case 
 

 done  No genes called significant under class1 < class2 

No genes called significant under class1 > class2 

Rank Product analysis for unpaired case 
 

 done  No genes called significant under class1 < class2 

Table2: Genes called significant under class1 > class2 

[ FAIL 0 | WARN 43 | SKIP 6 | PASS 209 ]

══ Skipped tests (6) ═══════════════════════════════════════════════════════════
• This test is skipped. (6): 'test-PomaLMM.R:3:3', 'test-PomaLMM.R:12:3',
  'test-PomaLMM.R:18:3', 'test-PomaLMM.R:27:3', 'test-PomaLMM.R:34:3',
  'test-PomaLMM.R:40:3'

[ FAIL 0 | WARN 43 | SKIP 6 | PASS 209 ]
> 
> proc.time()
   user  system elapsed 
 77.846   1.196  79.177 

Example timings

POMA.Rcheck/POMA-Ex.timings

nameusersystemelapsed
PomaBatch15.760 0.95816.755
PomaBoxplots23.008 0.52723.586
PomaClust1.1700.0321.205
PomaCorr2.5910.0162.612
PomaCreateObject0.4310.0370.570
PomaDensity2.4850.1592.651
PomaHeatmap9.3370.4319.794
PomaImpute0.0750.0040.078
PomaLM0.8590.0360.896
PomaLMM19.269 0.36719.692
PomaLasso2.4130.0442.461
PomaLimma0.1410.0000.142
PomaNorm0.0660.0000.066
PomaOddsRatio0.3570.0000.358
PomaOutliers0.9040.0120.918
PomaPCA1.0810.0161.101
PomaPCR0.3980.0030.402
PomaPLS22.628 1.12423.804
PomaRandForest0.6120.0360.650
PomaRankProd1.9370.0511.994
PomaUMAP4.8590.1925.068
PomaUnivariate63.757 0.56364.455
PomaVolcano0.4260.0040.430
theme_poma0.0010.0000.000