Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-12-23 12:06 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (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 1493/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
pairedGSEA 1.6.0 (landing page) Søren Helweg Dam
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino8 | 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 pairedGSEA package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/pairedGSEA.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: pairedGSEA |
Version: 1.6.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:pairedGSEA.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings pairedGSEA_1.6.0.tar.gz |
StartedAt: 2024-12-20 07:21:36 -0500 (Fri, 20 Dec 2024) |
EndedAt: 2024-12-20 07:36:57 -0500 (Fri, 20 Dec 2024) |
EllapsedTime: 920.8 seconds |
RetCode: 0 |
Status: OK |
CheckDir: pairedGSEA.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:pairedGSEA.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings pairedGSEA_1.6.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/pairedGSEA.Rcheck’ * using R version 4.4.2 (2024-10-31) * using platform: x86_64-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 Monterey 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘pairedGSEA/DESCRIPTION’ ... OK * this is package ‘pairedGSEA’ version ‘1.6.0’ * 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 ‘pairedGSEA’ 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 paired_diff 29.259 0.425 30.961 prepare_msigdb 10.301 0.593 10.959 * 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
pairedGSEA.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL pairedGSEA ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * installing *source* package ‘pairedGSEA’ ... ** 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 (pairedGSEA)
pairedGSEA.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: x86_64-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. > # > # Where should you do additional test configuration? > # Learn more about the roles of various files in: > # * https://r-pkgs.org/tests.html > # * https://testthat.r-lib.org/reference/test_package.html#special-files > > library(testthat) > suppressPackageStartupMessages(library("pairedGSEA")) > data("example_se", "example_ora_results", "example_diff_result", package = "pairedGSEA") > test_check("pairedGSEA") Running Example Preparing metadata Running SVA No significant surrogate variables Found 0 surrogate variables Running DESeq2 estimating size factors estimating dispersions gene-wise dispersion estimates mean-dispersion relationship final dispersion estimates fitting model and testing Stored DESeqDataSet in results/Example_dds.RDS Extracting results Stored differential expression results in results/Example_expression_results.RDS Initiating DEXSeq Creating DEXSeqDataSet converting counts to integer mode Stored DEXSeqDataSet in results/Example_dxd.RDS Running DEXSeq -- This might take a while Stored differential splicing results in results/Example_splicing_results.RDS Example is analysed. Aggregating p values Stored gene pvalue aggregation in results/Example_aggregated_pvals.RDS Done. No significant surrogate variables converting counts to integer mode No significant surrogate variables converting counts to integer mode No significant surrogate variables OBS: your design will be overwritten to: ~source No significant surrogate variables converting counts to integer mode No significant surrogate variables converting counts to integer mode converting counts to integer mode converting counts to integer mode converting counts to integer mode Running SVA Number of significant surrogate variables is: 2 Iteration (out of 5 ):1 2 3 4 5 Found 2 surrogate variables Redefining DESeq2 design formula Running over-representation analyses Joining result Running over-representation analyses Running over-representation analyses Joining result Storing fora results Stored ORA on differential analysis results in results/test_ora.RDS Running over-representation analyses Storing fora results Stored ORA on only DESeq2 results in results/test_ora.RDS Running Preparing metadata Removing 0 rows with a summed count lower than 10 Removing 108 rows with counts in less than 2 samples. Running SVA Number of significant surrogate variables is: 2 Iteration (out of 5 ):1 2 3 4 5 Found 2 surrogate variables Redefining DESeq2 design formula Running limma+voom Total number of exons: 5503 Total number of genes: 955 Number of genes with 1 exon: 142 Mean number of exons in a gene: 6 Max number of exons in a gene: 36 Aggregating p values Done. Running over-representation analyses Joining result converting counts to integer mode converting counts to integer mode Removing 1 rows with a summed count lower than 30 Removing 1 rows with counts in less than 2 samples. Removing 0 rows with a summed count lower than 1 Removing 1 rows with counts in less than 2 samples. Stored results in results/test_result.RDS Stored results in results/test_result.csv Stored results in results/test_result.xlsx Stored results in results/test_result.rdata Stored results in results/test_result.tsv [ FAIL 0 | WARN 0 | SKIP 1 | PASS 142 ] ══ Skipped tests (1) ═══════════════════════════════════════════════════════════ • empty test (1): 'test-utils.R:6:1' [ FAIL 0 | WARN 0 | SKIP 1 | PASS 142 ] > > proc.time() user system elapsed 291.696 3.568 304.037
pairedGSEA.Rcheck/pairedGSEA-Ex.timings
name | user | system | elapsed | |
paired_diff | 29.259 | 0.425 | 30.961 | |
paired_ora | 0.219 | 0.011 | 0.244 | |
plot_ora | 1.719 | 0.024 | 1.767 | |
prepare_msigdb | 10.301 | 0.593 | 10.959 | |