Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-05-04 11:37:53 -0400 (Sat, 04 May 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" | 4753 |
palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 beta (2024-04-15 r86425 ucrt) -- "Puppy Cup" | 4486 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 beta (2024-04-14 r86421) -- "Puppy Cup" | 4519 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" | 4479 |
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 912/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
graphite 1.50.0 (landing page) Gabriele Sales
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | ERROR | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | ERROR | ||||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | see weekly results here | ||||||||||||
To the developers/maintainers of the graphite package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/graphite.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: graphite |
Version: 1.50.0 |
Command: F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:graphite.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings graphite_1.50.0.tar.gz |
StartedAt: 2024-05-04 04:08:12 -0400 (Sat, 04 May 2024) |
EndedAt: 2024-05-04 04:13:29 -0400 (Sat, 04 May 2024) |
EllapsedTime: 317.2 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: graphite.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:graphite.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings graphite_1.50.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/graphite.Rcheck' * using R version 4.4.0 beta (2024-04-15 r86425 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 'graphite/DESCRIPTION' ... OK * this is package 'graphite' version '1.50.0' * 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 'graphite' 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 sizes of PDF files under 'inst/doc' ... OK * checking files in 'vignettes' ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed runTopologyGSA 11.82 0.50 13.06 runSPIA 6.94 2.03 47.22 convertIdentifiers 5.62 0.14 21.61 * 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: 1. └─graphite::pathways("hsapiens", "kegg") at test_spia.R:38:3 2. └─graphite:::loadData(paste(species, database, sep = "-")) 3. └─graphite:::fetchRemote(name, path) ── Error ('test_topologygsa.R:37:3'): (code run outside of `test_that()`) ────── Error in `fetchRemote(name, path)`: cannot download pathway data: are you offline? Backtrace: ▆ 1. └─graphite (local) load_pathways() at test_topologygsa.R:47:1 2. └─graphite::pathways("hsapiens", "kegg") at test_topologygsa.R:37:3 3. └─graphite:::loadData(paste(species, database, sep = "-")) 4. └─graphite:::fetchRemote(name, path) [ FAIL 5 | WARN 0 | SKIP 0 | PASS 75 ] Error: Test failures Execution halted * 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: 1 ERROR See 'F:/biocbuild/bbs-3.19-bioc/meat/graphite.Rcheck/00check.log' for details.
graphite.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL graphite ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.19-bioc/R/library' * installing *source* package 'graphite' ... ** using staged installation ** R ** 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 (graphite)
graphite.Rcheck/tests/testthat.Rout.fail
R version 4.4.0 beta (2024-04-15 r86425 ucrt) -- "Puppy Cup" 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(graphite) > > test_check("graphite") Error in curl::curl_fetch_disk(url, x$path, handle = handle) : Timeout was reached: [graphiteweb.bio.unipd.it] Failed to connect to graphiteweb.bio.unipd.it port 443 after 10015 ms: Timeout was reached Error in curl::curl_fetch_disk(url, x$path, handle = handle) : Timeout was reached: [graphiteweb.bio.unipd.it] Failed to connect to graphiteweb.bio.unipd.it port 443 after 10008 ms: Timeout was reached Error in curl::curl_fetch_disk(url, x$path, handle = handle) : Timeout was reached: [graphiteweb.bio.unipd.it] Failed to connect to graphiteweb.bio.unipd.it port 443 after 10008 ms: Timeout was reached Error in curl::curl_fetch_disk(url, x$path, handle = handle) : Timeout was reached: [graphiteweb.bio.unipd.it] Failed to connect to graphiteweb.bio.unipd.it port 443 after 10102 ms: Timeout was reached Error in curl::curl_fetch_disk(url, x$path, handle = handle) : Timeout was reached: [graphiteweb.bio.unipd.it] Failed to connect to graphiteweb.bio.unipd.it port 443 after 10014 ms: Timeout was reached [ FAIL 5 | WARN 0 | SKIP 0 | PASS 75 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test_fetch.R:24:3'): Mus musculus pathways can be downloaded ──────── Error in `fetchRemote(name, path)`: cannot download pathway data: are you offline? Backtrace: ▆ 1. └─graphite::pathways("mmusculus", "kegg") at test_fetch.R:24:3 2. └─graphite:::loadData(paste(species, database, sep = "-")) 3. └─graphite:::fetchRemote(name, path) ── Error ('test_graph.R:102:3'): graphNEL includes metabolites from pathway ──── Error in `fetchRemote(name, path)`: cannot download pathway data: are you offline? Backtrace: ▆ 1. └─graphite::pathways("hsapiens", "kegg") at test_graph.R:102:3 2. └─graphite:::loadData(paste(species, database, sep = "-")) 3. └─graphite:::fetchRemote(name, path) ── Error ('test_graph.R:110:3'): Selection of an invalid type of edge is rejected ── Error in `fetchRemote(name, path)`: cannot download pathway data: are you offline? Backtrace: ▆ 1. └─graphite::pathways("hsapiens", "kegg") at test_graph.R:110:3 2. └─graphite:::loadData(paste(species, database, sep = "-")) 3. └─graphite:::fetchRemote(name, path) ── Error ('test_spia.R:38:3'): analysis result contains one row for each pathway ── Error in `fetchRemote(name, path)`: cannot download pathway data: are you offline? Backtrace: ▆ 1. └─graphite::pathways("hsapiens", "kegg") at test_spia.R:38:3 2. └─graphite:::loadData(paste(species, database, sep = "-")) 3. └─graphite:::fetchRemote(name, path) ── Error ('test_topologygsa.R:37:3'): (code run outside of `test_that()`) ────── Error in `fetchRemote(name, path)`: cannot download pathway data: are you offline? Backtrace: ▆ 1. └─graphite (local) load_pathways() at test_topologygsa.R:47:1 2. └─graphite::pathways("hsapiens", "kegg") at test_topologygsa.R:37:3 3. └─graphite:::loadData(paste(species, database, sep = "-")) 4. └─graphite:::fetchRemote(name, path) [ FAIL 5 | WARN 0 | SKIP 0 | PASS 75 ] Error: Test failures Execution halted
graphite.Rcheck/graphite-Ex.timings
name | user | system | elapsed | |
Pathway-class | 3.44 | 0.05 | 3.50 | |
as.list.PathwayList | 0.63 | 0.06 | 0.72 | |
buildPathway | 0 | 0 | 0 | |
convertIdentifiers | 5.62 | 0.14 | 21.61 | |
cytoscapePlot | 0.00 | 0.02 | 0.02 | |
pathwayDatabases | 0 | 0 | 0 | |
pathwayGraph | 3.57 | 0.09 | 3.65 | |
pathways | 4.04 | 0.06 | 4.14 | |
runSPIA | 6.94 | 2.03 | 47.22 | |
runTopologyGSA | 11.82 | 0.50 | 13.06 | |