Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2025-10-13 11:40 -0400 (Mon, 13 Oct 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4833 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4614 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4555 |
kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4586 |
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 799/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
GeDi 1.4.0 (landing page) Annekathrin Nedwed
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | ERROR | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | ERROR | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | ERROR | OK | |||||||||
kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | ERROR | ||||||||||
To the developers/maintainers of the GeDi package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GeDi.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: GeDi |
Version: 1.4.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:GeDi.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings GeDi_1.4.0.tar.gz |
StartedAt: 2025-10-10 23:13:50 -0400 (Fri, 10 Oct 2025) |
EndedAt: 2025-10-10 23:28:33 -0400 (Fri, 10 Oct 2025) |
EllapsedTime: 883.0 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: GeDi.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:GeDi.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings GeDi_1.4.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/GeDi.Rcheck’ * using R version 4.5.1 Patched (2025-06-14 r88325) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 16.0.0 (clang-1600.0.26.6) GNU Fortran (GCC) 14.2.0 * running under: macOS Ventura 13.7.5 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘GeDi/DESCRIPTION’ ... OK * this is package ‘GeDi’ version ‘1.4.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... INFO Imports includes 29 non-default packages. Importing from so many packages makes the package vulnerable to any of them becoming unavailable. Move as many as possible to Suggests and use conditionally. * 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 ‘GeDi’ 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 ... 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 ... NOTE Found the following Rd file(s) with Rd \link{} targets missing package anchors: buildClusterGraph.Rd: igraph dot-graphMetricsGenesetsDT.Rd: igraph getAnnotation.Rd: STRINGdb getId.Rd: STRINGdb getPPI.Rd: STRINGdb getStringDB.Rd: STRINGdb Please provide package anchors for all Rd \link{} targets not in the package itself and the base packages. * 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 getAnnotation 142.297 4.391 152.471 getPPI 91.309 2.899 95.508 goDistance 6.244 0.637 7.239 scaleGO 5.727 0.488 6.530 * 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: [ FAIL 4 | WARN 9 | SKIP 0 | PASS 181 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test-distance_dendro.R:11:3'): distanceDendro runs correctly ────── `dendro` has type 'object', not 'list'. ── Failure ('test-distance_dendro.R:15:3'): distanceDendro runs correctly ────── `dendro` has type 'object', not 'list'. ── Failure ('test-gs_histogram.R:27:3'): gsHistogram runs correctly ──────────── `histogram` has type 'object', not 'list'. ── Failure ('test-gs_histogram.R:30:3'): gsHistogram runs correctly ──────────── `histogram` has type 'object', not 'list'. [ FAIL 4 | WARN 9 | SKIP 0 | PASS 181 ] 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, 1 NOTE See ‘/Users/biocbuild/bbs-3.21-bioc/meat/GeDi.Rcheck/00check.log’ for details.
GeDi.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL GeDi ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’ * installing *source* package ‘GeDi’ ... ** this is package ‘GeDi’ version ‘1.4.0’ ** 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 (GeDi)
GeDi.Rcheck/tests/testthat.Rout.fail
R version 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: aarch64-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. > library(testthat) > library(GeDi) > > test_check("GeDi") trying URL 'https://stringdb-downloads.org/download/protein.aliases.v12.0/9606.protein.aliases.v12.0.txt.gz' Content type 'application/octet-stream' length 19777800 bytes (18.9 MB) ================================================== downloaded 18.9 MB trying URL 'https://stringdb-downloads.org/download/protein.info.v12.0/9606.protein.info.v12.0.txt.gz' Content type 'application/octet-stream' length 1970090 bytes (1.9 MB) ================================================== downloaded 1.9 MB trying URL 'https://stringdb-downloads.org/download/protein.links.v12.0/9606.protein.links.v12.0.txt.gz' Content type 'application/octet-stream' length 83164437 bytes (79.3 MB) ================================================== downloaded 79.3 MB preparing gene to GO mapping data... preparing gene to GO mapping data... [ FAIL 4 | WARN 9 | SKIP 0 | PASS 181 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test-distance_dendro.R:11:3'): distanceDendro runs correctly ────── `dendro` has type 'object', not 'list'. ── Failure ('test-distance_dendro.R:15:3'): distanceDendro runs correctly ────── `dendro` has type 'object', not 'list'. ── Failure ('test-gs_histogram.R:27:3'): gsHistogram runs correctly ──────────── `histogram` has type 'object', not 'list'. ── Failure ('test-gs_histogram.R:30:3'): gsHistogram runs correctly ──────────── `histogram` has type 'object', not 'list'. [ FAIL 4 | WARN 9 | SKIP 0 | PASS 181 ] Error: Test failures Execution halted
GeDi.Rcheck/GeDi-Ex.timings
name | user | system | elapsed | |
GeDi | 0.010 | 0.002 | 0.012 | |
buildClusterGraph | 0.288 | 0.006 | 0.296 | |
buildGraph | 0.008 | 0.001 | 0.009 | |
buildHistogramData | 0.010 | 0.001 | 0.012 | |
calculateJaccard | 0.009 | 0.001 | 0.010 | |
calculateKappa | 0.023 | 0.001 | 0.025 | |
calculateSorensenDice | 0.009 | 0.002 | 0.011 | |
checkInclusion | 0.009 | 0.002 | 0.011 | |
clustering | 0.212 | 0.006 | 0.219 | |
deprecated | 0 | 0 | 0 | |
distanceDendro | 0.243 | 0.011 | 0.253 | |
distanceHeatmap | 0.241 | 0.012 | 0.254 | |
enrichmentWordcloud | 0.294 | 0.010 | 0.305 | |
fuzzyClustering | 0.007 | 0.002 | 0.009 | |
getAdjacencyMatrix | 0.054 | 0.003 | 0.057 | |
getAnnotation | 142.297 | 4.391 | 152.471 | |
getBipartiteGraph | 0.005 | 0.001 | 0.008 | |
getClusterAdjacencyMatrix | 0.091 | 0.003 | 0.096 | |
getGraphTitle | 0.004 | 0.001 | 0.004 | |
getId | 0.159 | 0.009 | 0.526 | |
getInteractionScore | 0.017 | 0.016 | 0.034 | |
getJaccardMatrix | 2.131 | 0.052 | 2.224 | |
getKappaMatrix | 0.905 | 0.112 | 1.135 | |
getMeetMinMatrix | 0.826 | 0.106 | 1.050 | |
getPPI | 91.309 | 2.899 | 95.508 | |
getSorensenDiceMatrix | 1.004 | 0.025 | 1.052 | |
getStringDB | 0.126 | 0.009 | 0.538 | |
getpMMMatrix | 0.813 | 0.071 | 0.908 | |
goDistance | 6.244 | 0.637 | 7.239 | |
gsHistogram | 0.121 | 0.020 | 0.153 | |
kMeansClustering | 0.021 | 0.010 | 0.033 | |
kNN_clustering | 0.011 | 0.009 | 0.020 | |
louvainClustering | 0.063 | 0.016 | 0.086 | |
markovClustering | 0.074 | 0.017 | 0.093 | |
pMMlocal | 0.039 | 0.021 | 0.062 | |
pamClustering | 0.01 | 0.01 | 0.02 | |
prepareGenesetData | 0.010 | 0.008 | 0.019 | |
scaleGO | 5.727 | 0.488 | 6.530 | |
seedFinding | 0.010 | 0.008 | 0.020 | |