Pol Castellano-Escuder
| Snapshot Date: 2024-10-16 14:00 -0400 (Wed, 16 Oct 2024) |
| git_url: https://git.bioconductor.org/packages/POMA |
| git_branch: RELEASE_3_19 |
| git_last_commit: 1a5a6e4 |
| git_last_commit_date: 2024-04-30 11:25:46 -0400 (Tue, 30 Apr 2024) |
| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-10-18 20:39 -0400 (Fri, 18 Oct 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4763 |
| palomino7 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4500 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4530 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 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 1592/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| POMA 1.14.0 (landing page) Pol Castellano-Escuder
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | 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 | | ||||||||
|
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. |
| Package: POMA |
| Version: 1.14.0 |
| Command: E:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:POMA.install-out.txt --library=E:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings POMA_1.14.0.tar.gz |
| StartedAt: 2024-10-17 04:33:45 -0400 (Thu, 17 Oct 2024) |
| EndedAt: 2024-10-17 04:38:27 -0400 (Thu, 17 Oct 2024) |
| EllapsedTime: 281.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: POMA.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### E:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:POMA.install-out.txt --library=E:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings POMA_1.14.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'E:/biocbuild/bbs-3.19-bioc/meat/POMA.Rcheck'
* using R version 4.4.1 (2024-06-14 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
gcc.exe (GCC) 13.2.0
GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* 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 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 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 62.54 0.27 62.84
PomaBoxplots 20.34 0.72 21.08
PomaPLS 18.22 0.44 18.67
PomaLMM 14.85 0.09 14.94
PomaBatch 12.00 0.49 12.54
PomaHeatmap 8.52 0.75 8.67
* 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
'E:/biocbuild/bbs-3.19-bioc/meat/POMA.Rcheck/00check.log'
for details.
POMA.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### E:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL POMA ### ############################################################################## ############################################################################## * installing to library 'E:/biocbuild/bbs-3.19-bioc/R/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)
POMA.Rcheck/tests/testthat.Rout
R version 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64
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 37 | 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 37 | SKIP 6 | PASS 209 ]
>
> proc.time()
user system elapsed
67.53 2.53 69.23
POMA.Rcheck/POMA-Ex.timings
| name | user | system | elapsed | |
| PomaBatch | 12.00 | 0.49 | 12.54 | |
| PomaBoxplots | 20.34 | 0.72 | 21.08 | |
| PomaClust | 0.75 | 0.03 | 0.78 | |
| PomaCorr | 1.47 | 0.03 | 1.50 | |
| PomaCreateObject | 0.33 | 0.03 | 0.45 | |
| PomaDensity | 2.20 | 0.06 | 2.27 | |
| PomaHeatmap | 8.52 | 0.75 | 8.67 | |
| PomaImpute | 0.06 | 0.00 | 0.06 | |
| PomaLM | 0.59 | 0.02 | 0.61 | |
| PomaLMM | 14.85 | 0.09 | 14.94 | |
| PomaLasso | 1.86 | 0.01 | 1.87 | |
| PomaLimma | 0.09 | 0.00 | 0.09 | |
| PomaNorm | 0.03 | 0.02 | 0.05 | |
| PomaOddsRatio | 0.27 | 0.00 | 0.27 | |
| PomaOutliers | 0.83 | 0.04 | 0.88 | |
| PomaPCA | 0.95 | 0.00 | 0.95 | |
| PomaPCR | 0.37 | 0.00 | 0.37 | |
| PomaPLS | 18.22 | 0.44 | 18.67 | |
| PomaRandForest | 0.55 | 0.00 | 0.55 | |
| PomaRankProd | 1.59 | 0.06 | 1.67 | |
| PomaUMAP | 4.50 | 0.02 | 4.58 | |
| PomaUnivariate | 62.54 | 0.27 | 62.84 | |
| PomaVolcano | 0.32 | 0.00 | 0.33 | |
| theme_poma | 0 | 0 | 0 | |