| Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-10-24 12:03 -0400 (Fri, 24 Oct 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4898 |
| lconway | macOS 12.7.6 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4688 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4634 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4658 |
| 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 808/2359 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| GeDi 1.5.0 (landing page) Annekathrin Nedwed
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | ERROR | |||||||||
| lconway | macOS 12.7.6 Monterey / x86_64 | OK | OK | ERROR | OK | |||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | ERROR | OK | |||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | NA | ||||||||||
|
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: 1.5.0 |
| Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:GeDi.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings GeDi_1.5.0.tar.gz |
| StartedAt: 2025-10-23 23:46:38 -0400 (Thu, 23 Oct 2025) |
| EndedAt: 2025-10-24 00:03:22 -0400 (Fri, 24 Oct 2025) |
| EllapsedTime: 1003.9 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: GeDi.Rcheck |
| Warnings: NA |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:GeDi.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings GeDi_1.5.0.tar.gz
###
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##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/GeDi.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘GeDi/DESCRIPTION’ ... OK
* this is package ‘GeDi’ version ‘1.5.0’
* 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 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 ... 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 96.839 9.357 195.363
getPPI 70.648 3.134 74.292
scaleGO 6.712 0.669 7.382
goDistance 6.073 0.970 7.042
getId 0.386 0.084 5.261
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 ERROR, 1 NOTE
See
‘/home/biocbuild/bbs-3.22-bioc/meat/GeDi.Rcheck/00check.log’
for details.
GeDi.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL GeDi ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’ * installing *source* package ‘GeDi’ ... ** this is package ‘GeDi’ version ‘1.5.0’ ** 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 (2025-08-23 r88802) -- "Great Square Root"
Copyright (C) 2025 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(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 | 0.006 | 0.000 | 0.006 | |
| buildClusterGraph | 0.197 | 0.018 | 0.216 | |
| buildGraph | 0.005 | 0.000 | 0.006 | |
| buildHistogramData | 0.007 | 0.000 | 0.008 | |
| calculateJaccard | 0.005 | 0.001 | 0.007 | |
| calculateKappa | 0.013 | 0.000 | 0.014 | |
| calculateSorensenDice | 0.006 | 0.001 | 0.007 | |
| checkInclusion | 0.007 | 0.000 | 0.007 | |
| clustering | 0.146 | 0.000 | 0.145 | |
| deprecated | 0 | 0 | 0 | |
| distanceDendro | 0.152 | 0.000 | 0.153 | |
| distanceHeatmap | 0.121 | 0.001 | 0.122 | |
| enrichmentWordcloud | 0.232 | 0.013 | 0.245 | |
| fuzzyClustering | 0.004 | 0.003 | 0.007 | |
| getAdjacencyMatrix | 0.098 | 0.004 | 0.102 | |
| getAnnotation | 96.839 | 9.357 | 195.363 | |
| getBipartiteGraph | 0.011 | 0.005 | 0.015 | |
| getClusterAdjacencyMatrix | 0.066 | 0.015 | 0.081 | |
| getGraphTitle | 0.003 | 0.002 | 0.005 | |
| getId | 0.386 | 0.084 | 5.261 | |
| getInteractionScore | 0.050 | 0.007 | 0.057 | |
| getJaccardMatrix | 1.151 | 0.161 | 1.312 | |
| getKappaMatrix | 3.851 | 0.509 | 4.359 | |
| getMeetMinMatrix | 0.718 | 0.019 | 0.737 | |
| getPPI | 70.648 | 3.134 | 74.292 | |
| getSorensenDiceMatrix | 0.444 | 0.000 | 0.444 | |
| getStringDB | 0.386 | 0.029 | 3.397 | |
| getpMMMatrix | 0.914 | 0.098 | 1.011 | |
| goDistance | 6.073 | 0.970 | 7.042 | |
| gsHistogram | 0.101 | 0.007 | 0.107 | |
| kMeansClustering | 0.010 | 0.004 | 0.013 | |
| kNN_clustering | 0.008 | 0.000 | 0.008 | |
| louvainClustering | 0.052 | 0.005 | 0.056 | |
| markovClustering | 0.065 | 0.003 | 0.068 | |
| pMMlocal | 0.030 | 0.000 | 0.031 | |
| pamClustering | 0.006 | 0.000 | 0.007 | |
| prepareGenesetData | 0.006 | 0.002 | 0.008 | |
| scaleGO | 6.712 | 0.669 | 7.382 | |
| seedFinding | 0.006 | 0.000 | 0.006 | |