Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2025-01-23 12:05 -0500 (Thu, 23 Jan 2025).
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" | 4746 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4493 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4517 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4469 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4394 |
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 1367/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
multiGSEA 1.16.2 (landing page) Sebastian Canzler
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | ERROR | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | TIMEOUT | skipped | skipped | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | |||||||||
taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | TIMEOUT | skipped | ||||||||||
To the developers/maintainers of the multiGSEA package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/multiGSEA.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: multiGSEA |
Version: 1.16.2 |
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:multiGSEA.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings multiGSEA_1.16.2.tar.gz |
StartedAt: 2025-01-21 00:15:34 -0500 (Tue, 21 Jan 2025) |
EndedAt: 2025-01-21 00:25:58 -0500 (Tue, 21 Jan 2025) |
EllapsedTime: 624.8 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: multiGSEA.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:multiGSEA.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings multiGSEA_1.16.2.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/multiGSEA.Rcheck’ * using R version 4.4.2 (2024-10-31) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 * running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * checking for file ‘multiGSEA/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘multiGSEA’ version ‘1.16.2’ * 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 ‘multiGSEA’ 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 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 ... ERROR Running examples in ‘multiGSEA-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: extractPvalues > ### Title: Create a reshaped data frame from multiGSEA output. > ### Aliases: extractPvalues > > ### ** Examples > > # Download pathway definition and extract features > pathways <- getMultiOmicsFeatures(dbs = c("kegg"), layer = c("transcriptome", "proteome")) Error in curl::curl_fetch_disk(url, x$path, handle = handle) : Timeout was reached [graphiteweb.bio.unipd.it]: SSL connection timeout Error in fetchRemote(name, path) : cannot download pathway data: are you offline? Calls: getMultiOmicsFeatures ... lapply -> FUN -> <Anonymous> -> loadData -> fetchRemote Execution halted * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: 6. └─graphite:::fetchRemote(name, path) ── Error ('test_pathway_features.R:45:3'): each layer has equal length ───────── Error in `fetchRemote(name, path)`: cannot download pathway data: are you offline? Backtrace: ▆ 1. └─multiGSEA::getMultiOmicsFeatures(dbs = dbs, organism = "hsapiens") at test_pathway_features.R:45:3 2. └─base::lapply(...) 3. └─multiGSEA (local) FUN(X[[i]], ...) 4. └─graphite::pathways(organism, x) 5. └─graphite:::loadData(paste(species, database, sep = "-")) 6. └─graphite:::fetchRemote(name, path) [ FAIL 5 | WARN 0 | SKIP 0 | PASS 17 ] Error: Test failures Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... ERROR Error(s) in re-building vignettes: ... --- re-building ‘multiGSEA.rmd’ using rmarkdown Quitting from lines 269-279 [calculate_enrichment] (multiGSEA.rmd) Error: processing vignette 'multiGSEA.rmd' failed with diagnostics: cannot download pathway data: are you offline? --- failed re-building ‘multiGSEA.rmd’ SUMMARY: processing the following file failed: ‘multiGSEA.rmd’ Error: Vignette re-building failed. Execution halted * checking PDF version of manual ... OK * DONE Status: 3 ERRORs See ‘/home/biocbuild/bbs-3.20-bioc/meat/multiGSEA.Rcheck/00check.log’ for details.
multiGSEA.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL multiGSEA ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’ * installing *source* package ‘multiGSEA’ ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading loading from cache ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location loading from cache ** testing if installed package can be loaded from final location loading from cache ** testing if installed package keeps a record of temporary installation path * DONE (multiGSEA)
multiGSEA.Rcheck/tests/testthat.Rout.fail
R version 4.4.2 (2024-10-31) -- "Pile of Leaves" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-pc-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(multiGSEA) loading from cache > > test_check("multiGSEA") Error in curl::curl_fetch_disk(url, x$path, handle = handle) : Timeout was reached [graphiteweb.bio.unipd.it]: SSL connection timeout Error in curl::curl_fetch_disk(url, x$path, handle = handle) : Timeout was reached [graphiteweb.bio.unipd.it]: SSL connection timeout Error in curl::curl_fetch_disk(url, x$path, handle = handle) : Timeout was reached [graphiteweb.bio.unipd.it]: SSL connection timeout Error in curl::curl_fetch_disk(url, x$path, handle = handle) : Timeout was reached [graphiteweb.bio.unipd.it]: SSL connection timeout Error in curl::curl_fetch_disk(url, x$path, handle = handle) : Timeout was reached [graphiteweb.bio.unipd.it]: SSL connection timeout [ FAIL 5 | WARN 0 | SKIP 0 | PASS 17 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test_pathway_enrichment.R:34:3'): pathway enrichment works. ───────── Error in `fetchRemote(name, path)`: cannot download pathway data: are you offline? Backtrace: ▆ 1. └─multiGSEA::getMultiOmicsFeatures(dbs = dbs) at test_pathway_enrichment.R:34:3 2. └─base::lapply(...) 3. └─multiGSEA (local) FUN(X[[i]], ...) 4. └─graphite::pathways(organism, x) 5. └─graphite:::loadData(paste(species, database, sep = "-")) 6. └─graphite:::fetchRemote(name, path) ── Error ('test_pathway_features.R:7:3'): transcriptomic features get mapped ─── Error in `fetchRemote(name, path)`: cannot download pathway data: are you offline? Backtrace: ▆ 1. └─multiGSEA::getMultiOmicsFeatures(dbs = dbs, layer = layer) at test_pathway_features.R:7:3 2. └─base::lapply(...) 3. └─multiGSEA (local) FUN(X[[i]], ...) 4. └─graphite::pathways(organism, x) 5. └─graphite:::loadData(paste(species, database, sep = "-")) 6. └─graphite:::fetchRemote(name, path) ── Error ('test_pathway_features.R:20:3'): proteomic features get mapped ─────── Error in `fetchRemote(name, path)`: cannot download pathway data: are you offline? Backtrace: ▆ 1. └─multiGSEA::getMultiOmicsFeatures(dbs = dbs, layer = layer) at test_pathway_features.R:20:3 2. └─base::lapply(...) 3. └─multiGSEA (local) FUN(X[[i]], ...) 4. └─graphite::pathways(organism, x) 5. └─graphite:::loadData(paste(species, database, sep = "-")) 6. └─graphite:::fetchRemote(name, path) ── Error ('test_pathway_features.R:33:3'): metabolomic features get mapped ───── Error in `fetchRemote(name, path)`: cannot download pathway data: are you offline? Backtrace: ▆ 1. └─multiGSEA::getMultiOmicsFeatures(dbs = dbs, layer = layer) at test_pathway_features.R:33:3 2. └─base::lapply(...) 3. └─multiGSEA (local) FUN(X[[i]], ...) 4. └─graphite::pathways(organism, x) 5. └─graphite:::loadData(paste(species, database, sep = "-")) 6. └─graphite:::fetchRemote(name, path) ── Error ('test_pathway_features.R:45:3'): each layer has equal length ───────── Error in `fetchRemote(name, path)`: cannot download pathway data: are you offline? Backtrace: ▆ 1. └─multiGSEA::getMultiOmicsFeatures(dbs = dbs, organism = "hsapiens") at test_pathway_features.R:45:3 2. └─base::lapply(...) 3. └─multiGSEA (local) FUN(X[[i]], ...) 4. └─graphite::pathways(organism, x) 5. └─graphite:::loadData(paste(species, database, sep = "-")) 6. └─graphite:::fetchRemote(name, path) [ FAIL 5 | WARN 0 | SKIP 0 | PASS 17 ] Error: Test failures Execution halted
multiGSEA.Rcheck/multiGSEA-Ex.timings
name | user | system | elapsed | |
combinePvalues | 0.005 | 0.000 | 0.005 | |