Annekathrin Nedwed
| Snapshot Date: 2025-12-11 13:45 -0500 (Thu, 11 Dec 2025) |
| git_url: https://git.bioconductor.org/packages/GeDi |
| git_branch: RELEASE_3_22 |
| git_last_commit: 41a45ca |
| git_last_commit_date: 2025-11-26 10:23:10 -0500 (Wed, 26 Nov 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-12-15 12:09 -0500 (Mon, 15 Dec 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4882 |
| merida1 | macOS 12.7.6 Monterey | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4673 |
| kjohnson1 | macOS 13.7.5 Ventura | arm64 | 4.5.2 Patched (2025-11-04 r88984) -- "[Not] Part in a Rumble" | 4607 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4671 |
| 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 809/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| GeDi 1.6.1 (landing page) Annekathrin Nedwed
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.7.5 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| taishan | 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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: GeDi |
| Version: 1.6.1 |
| Command: /home/biocbuild/R/R/bin/R CMD check --install=check:GeDi.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings GeDi_1.6.1.tar.gz |
| StartedAt: 2025-12-12 10:22:39 -0000 (Fri, 12 Dec 2025) |
| EndedAt: 2025-12-12 10:41:28 -0000 (Fri, 12 Dec 2025) |
| EllapsedTime: 1128.3 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: GeDi.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R/bin/R CMD check --install=check:GeDi.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings GeDi_1.6.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/GeDi.Rcheck’
* using R version 4.5.0 (2025-04-11)
* 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 ‘GeDi/DESCRIPTION’ ... OK
* this is package ‘GeDi’ version ‘1.6.1’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 30 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 loading without being on the library search path ... 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 ... 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
getAnnotation 97.241 5.533 291.525
getPPI 72.445 1.459 77.004
goDistance 27.673 0.442 28.602
* 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:
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-downloadPPI.R:28:3'): PPI retrieval works ──────────────────────
Error in `download.file(urlStr, temp)`: download from 'https://stringdb-downloads.org/download/protein.links.v12.0/9606.protein.links.v12.0.txt.gz' failed
Backtrace:
▆
1. └─GeDi::getPPI(genes, stringdb, anno_df) at test-downloadPPI.R:28:3
2. └─stringdb$get_interactions(string_ids)
3. └─STRINGdb (local) load()
4. └─STRINGdb::downloadAbsentFile(url, oD = input_directory)
5. └─utils::download.file(urlStr, temp)
[ FAIL 1 | WARN 2 | SKIP 0 | PASS 166 ]
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
‘/home/biocbuild/bbs-3.22-bioc/meat/GeDi.Rcheck/00check.log’
for details.
GeDi.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL GeDi ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’ * installing *source* package ‘GeDi’ ... ** this is package ‘GeDi’ version ‘1.6.1’ ** 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 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
Copyright (C) 2025 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.
> 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 41.2 MB
relations: is_a, part_of
term_sim_method: Sim_Wang_2007
removed 1 terms that cannot be found in the DAG.
[ FAIL 1 | WARN 2 | SKIP 0 | PASS 166 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-downloadPPI.R:28:3'): PPI retrieval works ──────────────────────
Error in `download.file(urlStr, temp)`: download from 'https://stringdb-downloads.org/download/protein.links.v12.0/9606.protein.links.v12.0.txt.gz' failed
Backtrace:
▆
1. └─GeDi::getPPI(genes, stringdb, anno_df) at test-downloadPPI.R:28:3
2. └─stringdb$get_interactions(string_ids)
3. └─STRINGdb (local) load()
4. └─STRINGdb::downloadAbsentFile(url, oD = input_directory)
5. └─utils::download.file(urlStr, temp)
[ FAIL 1 | WARN 2 | SKIP 0 | PASS 166 ]
Error: Test failures
Execution halted
GeDi.Rcheck/GeDi-Ex.timings
| name | user | system | elapsed | |
| GeDi | 0.008 | 0.000 | 0.007 | |
| buildClusterGraph | 0.126 | 0.004 | 0.131 | |
| buildGraph | 0.069 | 0.000 | 0.069 | |
| buildHistogramData | 0.01 | 0.00 | 0.01 | |
| checkInclusion | 0.011 | 0.000 | 0.011 | |
| clustering | 0.153 | 0.000 | 0.153 | |
| deprecated | 0 | 0 | 0 | |
| distanceDendro | 0.228 | 0.000 | 0.229 | |
| distanceHeatmap | 0.196 | 0.016 | 0.213 | |
| dot-cluster_markov | 0.527 | 0.036 | 0.563 | |
| dot-map_to_color | 0.02 | 0.00 | 0.02 | |
| enrichmentWordcloud | 0.296 | 0.008 | 0.307 | |
| fuzzyClustering | 0.005 | 0.004 | 0.010 | |
| getAdjacencyMatrix | 0.090 | 0.016 | 0.105 | |
| getAnnotation | 97.241 | 5.533 | 291.525 | |
| getBipartiteGraph | 0.012 | 0.000 | 0.012 | |
| getClusterAdjacencyMatrix | 0.021 | 0.007 | 0.029 | |
| getGraphTitle | 0.005 | 0.000 | 0.006 | |
| getId | 0.156 | 0.003 | 4.712 | |
| getInteractionScore | 0.031 | 0.004 | 0.036 | |
| getJaccardMatrix | 0.052 | 0.000 | 0.056 | |
| getKappaMatrix | 0.056 | 0.004 | 0.092 | |
| getMeetMinMatrix | 0.029 | 0.004 | 0.073 | |
| getPPI | 72.445 | 1.459 | 77.004 | |
| getSorensenDiceMatrix | 0.022 | 0.000 | 0.021 | |
| getStringDB | 0.109 | 0.020 | 3.328 | |
| getpMMMatrix | 1.836 | 0.083 | 2.111 | |
| goDistance | 27.673 | 0.442 | 28.602 | |
| gsHistogram | 0.147 | 0.000 | 0.148 | |
| kMeansClustering | 0.025 | 0.000 | 0.025 | |
| kNN_clustering | 0.010 | 0.000 | 0.011 | |
| louvainClustering | 0.156 | 0.000 | 0.161 | |
| markovClustering | 0.101 | 0.000 | 0.101 | |
| pMMlocal | 0.033 | 0.000 | 0.034 | |
| pamClustering | 0.007 | 0.000 | 0.008 | |
| path_to_GeDi | 0.055 | 0.000 | 0.056 | |
| prepareGenesetData | 0.009 | 0.000 | 0.010 | |
| seedFinding | 0.01 | 0.00 | 0.01 | |