Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2024-12-24 11:47 -0500 (Tue, 24 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4754 |
palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4472 |
lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4426 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4381 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4373 |
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 1568/2274 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
PolySTest 1.1.0 (landing page) Veit Schwämmle
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
To the developers/maintainers of the PolySTest package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/PolySTest.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: PolySTest |
Version: 1.1.0 |
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:PolySTest.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings PolySTest_1.1.0.tar.gz |
StartedAt: 2024-12-24 09:54:10 -0000 (Tue, 24 Dec 2024) |
EndedAt: 2024-12-24 10:04:17 -0000 (Tue, 24 Dec 2024) |
EllapsedTime: 606.8 seconds |
RetCode: 0 |
Status: OK |
CheckDir: PolySTest.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:PolySTest.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings PolySTest_1.1.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/PolySTest.Rcheck’ * using R Under development (unstable) (2024-11-24 r87369) * using platform: aarch64-unknown-linux-gnu * R was compiled by aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0 GNU Fortran (GCC) 14.2.0 * running under: openEuler 24.03 (LTS) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘PolySTest/DESCRIPTION’ ... OK * this is package ‘PolySTest’ version ‘1.1.0’ * 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 ‘PolySTest’ 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 ... NOTE File LICENSE is not mentioned in the DESCRIPTION file. * 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 ... NOTE perm_unpaired: no visible binding for global variable ‘NumTests’ permtest_paired: no visible binding for global variable ‘NumTests’ Undefined global functions or variables: NumTests * 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 PolySTest_unpaired 0.517 0.080 31.055 perm_unpaired 0.037 0.056 14.783 FindFCandQlim 0.015 0.004 11.397 permtest_paired 0.003 0.008 11.506 rp_unpaired 0.008 0.002 11.135 * 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-3.21-bioc/meat/PolySTest.Rcheck/00check.log’ for details.
PolySTest.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL PolySTest ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library’ * installing *source* package ‘PolySTest’ ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** 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 (PolySTest)
PolySTest.Rcheck/tests/testthat.Rout
R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" 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. > # > # Where should you do additional test configuration? > # Learn more about the roles of various files in: > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview > # * https://testthat.r-lib.org/articles/special-files.html > > library(testthat) > library(PolySTest) > > test_check("PolySTest") Estimating suitable values for FDR and FC cutoff Estimating suitable values for FDR and FC cutoff Loading required package: MatrixGenerics Loading required package: matrixStats Attaching package: 'MatrixGenerics' The following objects are masked from 'package:matrixStats': colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse, colCounts, colCummaxs, colCummins, colCumprods, colCumsums, colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs, colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats, colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds, colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads, colWeightedMeans, colWeightedMedians, colWeightedSds, colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet, rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods, rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps, rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins, rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks, rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars, rowWeightedMads, rowWeightedMeans, rowWeightedMedians, rowWeightedSds, rowWeightedVars Loading required package: GenomicRanges Loading required package: stats4 Loading required package: BiocGenerics Loading required package: generics Attaching package: 'generics' The following objects are masked from 'package:base': as.difftime, as.factor, as.ordered, intersect, is.element, setdiff, setequal, union Attaching package: 'BiocGenerics' The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, saveRDS, table, tapply, unique, unsplit, which.max, which.min Loading required package: S4Vectors Attaching package: 'S4Vectors' The following object is masked from 'package:utils': findMatches The following objects are masked from 'package:base': I, expand.grid, unname Loading required package: IRanges Loading required package: GenomeInfoDb Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Attaching package: 'Biobase' The following object is masked from 'package:MatrixGenerics': rowMedians The following objects are masked from 'package:matrixStats': anyMissing, rowMedians Plotting number of regulated features Running limma test limma completed Running Miss_Test test Running Miss test ... ================================================================================ Miss_Test completed =======tests completed Unifying q-values across tests ... Calculating PolySTest FDRs ... ------- Summary of Results -------- Number of differentially regulated features with FDR < 0.01: | | PolySTest| limma| Miss_Test| rank_products| permutation_test| t_test| |:------|---------:|-----:|---------:|-------------:|----------------:|------:| |B_vs_A | 0| 0| 0| 0| 0| 0| Running limma test limma completed =======tests completed ------- Summary of Results -------- Number of differentially regulated features with FDR < 0.01: | | limma| t_test| |:------|-----:|------:| |B_vs_A | 0| 0| Running limma test limma completed =======tests completed Unifying q-values across tests ... Calculating PolySTest FDRs ... ------- Summary of Results -------- Number of differentially regulated features with FDR < 0.01: | | PolySTest| limma| rank_products| t_test| |:------|---------:|-----:|-------------:|------:| |B_vs_A | 0| 0| 0| 0| Running limma test limma completed Running Miss_Test test Running Miss test ... ================================================================================ Miss_Test completed ================================================================================ tests completed Unifying q-values across tests ... Calculating PolySTest FDRs ... ------- Summary of Results -------- Number of differentially regulated features with FDR < 0.01: | | PolySTest| limma| Miss_Test| rank_products| permutation_test| t_test| |:------|---------:|-----:|---------:|-------------:|----------------:|------:| |B_vs_A | 0| 0| 0| 0| 0| 0| Running limma test limma completed ================================================================================ tests completed ------- Summary of Results -------- Number of differentially regulated features with FDR < 0.01: | | limma| t_test| |:------|-----:|------:| |B_vs_A | 0| 0| Running limma test limma completed ================================================================================ tests completed Unifying q-values across tests ... Calculating PolySTest FDRs ... ------- Summary of Results -------- Number of differentially regulated features with FDR < 0.01: | | PolySTest| limma| rank_products| t_test| |:------|---------:|-----:|-------------:|------:| |B_vs_A | 0| 0| 0| 0| All pairwise comparison between conditions: |Condition A |Condition B | |:-----------|:-----------| |TTA.Rep. |HF.Rep. | |TTA.Rep. |FO.Rep. | |TTA.Rep. |TTA.FO.Rep. | Running limma test limma completed Running Miss_Test test Running Miss test ... ================================================================================ Miss_Test completed ======================================================tests completed Unifying q-values across tests ... Calculating PolySTest FDRs ... ------- Summary of Results -------- Number of differentially regulated features with FDR < 0.01: | | PolySTest| limma| Miss_Test| rank_products| permutation_test| t_test| |:-----------------------|---------:|-----:|---------:|-------------:|----------------:|------:| |HF.Rep._vs_TTA.Rep. | 23| 33| 9| 3| 0| 0| |FO.Rep._vs_TTA.Rep. | 20| 39| 8| 4| 0| 0| |TTA.FO.Rep._vs_TTA.Rep. | 1| 0| 2| 0| 0| 0| Running limma test limma completed Running Miss_Test test Running Miss test ... ================================================================================ Miss_Test completed ================================================================================ tests completed Unifying q-values across tests ... Calculating PolySTest FDRs ... ------- Summary of Results -------- Number of differentially regulated features with FDR < 0.01: | | PolySTest| limma| Miss_Test| rank_products| permutation_test| t_test| |:-----------------------|---------:|-----:|---------:|-------------:|----------------:|------:| |HF.Rep._vs_TTA.Rep. | 34| 49| 7| 3| 0| 16| |FO.Rep._vs_TTA.Rep. | 33| 46| 7| 5| 0| 11| |TTA.FO.Rep._vs_TTA.Rep. | 1| 0| 2| 0| 0| 0| plotting expression profiles Making circos plot Note: 1 point is out of plotting region in sector '1', track '1'. Note: 1 point is out of plotting region in sector '1', track '1'. Note: 1 point is out of plotting region in sector '2', track '1'. Note: 1 point is out of plotting region in sector '2', track '1'. Note: 1 point is out of plotting region in sector '3', track '1'. Note: 1 point is out of plotting region in sector '3', track '1'. plotting expression profiles Making circos plot Note: 1 point is out of plotting region in sector '1', track '1'. Note: 1 point is out of plotting region in sector '1', track '1'. Note: 1 point is out of plotting region in sector '2', track '1'. Note: 1 point is out of plotting region in sector '2', track '1'. Note: 1 point is out of plotting region in sector '3', track '1'. Note: 1 point is out of plotting region in sector '3', track '1'. plotting heatmap ... plotting heatmap ... Plotting p-values Plotting upset plots Plotting volcano plots Plotting volcano plots [ FAIL 0 | WARN 0 | SKIP 0 | PASS 64 ] > > proc.time() user system elapsed 21.801 1.657 295.886
PolySTest.Rcheck/PolySTest-Ex.timings
name | user | system | elapsed | |
FindFCandQlim | 0.015 | 0.004 | 11.397 | |
FindFCandQlimAlternative | 0.003 | 0.000 | 0.003 | |
MissValPDistr | 0.000 | 0.000 | 0.001 | |
MissingStats | 0.022 | 0.008 | 0.030 | |
MissingStatsDesign | 0.050 | 0.008 | 0.059 | |
PolySTest_paired | 0.535 | 0.044 | 0.580 | |
PolySTest_unpaired | 0.517 | 0.080 | 31.055 | |
RPStats | 0.001 | 0.000 | 0.001 | |
StatsForPermutTest | 0.000 | 0.000 | 0.001 | |
check_for_polystest | 0.023 | 0.007 | 0.030 | |
check_stat_names | 0.012 | 0.000 | 0.011 | |
create_pairwise_comparisons | 0.004 | 0.000 | 0.004 | |
get_numthreads | 0 | 0 | 0 | |
limma_paired | 0.021 | 0.004 | 0.025 | |
limma_unpaired | 0.019 | 0.000 | 0.019 | |
liver_example | 0.011 | 0.000 | 0.011 | |
perm_unpaired | 0.037 | 0.056 | 14.783 | |
permtest_paired | 0.003 | 0.008 | 11.506 | |
plotExpression | 4.260 | 0.311 | 4.583 | |
plotHeatmaply | 2.492 | 0.057 | 2.553 | |
plotPvalueDistr | 0.071 | 0.000 | 0.071 | |
plotRegNumber | 0.279 | 0.000 | 0.279 | |
plotUpset | 0.937 | 0.039 | 0.980 | |
plotVolcano | 0.046 | 0.003 | 0.050 | |
rp_unpaired | 0.008 | 0.002 | 11.135 | |
set_mfrow | 0.028 | 0.000 | 0.028 | |
ttest_paired | 0.024 | 0.000 | 0.024 | |
ttest_unpaired | 0.033 | 0.003 | 0.037 | |
update_conditions_with_lcs | 0.266 | 0.012 | 0.279 | |