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This page was generated on 2025-09-15 12:04 -0400 (Mon, 15 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4719
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4538
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4522
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4543
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 798/2327HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GeDi 1.5.0  (landing page)
Annekathrin Nedwed
Snapshot Date: 2025-09-14 13:45 -0400 (Sun, 14 Sep 2025)
git_url: https://git.bioconductor.org/packages/GeDi
git_branch: devel
git_last_commit: 54df8c8
git_last_commit_date: 2025-04-15 13:33:55 -0400 (Tue, 15 Apr 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    ERROR  
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    ERROR    OK  
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    ERROR    OK  
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    ERROR  


CHECK results for GeDi on lconway

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.

raw results


Summary

Package: GeDi
Version: 1.5.0
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_1.5.0.tar.gz
StartedAt: 2025-09-14 21:00:59 -0400 (Sun, 14 Sep 2025)
EndedAt: 2025-09-14 21:17:41 -0400 (Sun, 14 Sep 2025)
EllapsedTime: 1001.6 seconds
RetCode: 1
Status:   ERROR  
CheckDir: GeDi.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### 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_1.5.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/GeDi.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* 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 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    114.413  5.022 207.616
getPPI            76.110  1.654  78.558
getMeetMinMatrix   5.573  0.708   6.328
goDistance         5.787  0.483   6.331
scaleGO            5.777  0.452   6.292
* 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-3.22-bioc/meat/GeDi.Rcheck/00check.log’
for details.


Installation output

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-x86_64/Resources/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)

Tests output

GeDi.Rcheck/tests/testthat.Rout.fail


R version 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-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

Example timings

GeDi.Rcheck/GeDi-Ex.timings

nameusersystemelapsed
GeDi0.0070.0020.008
buildClusterGraph0.2080.0060.215
buildGraph0.0050.0010.006
buildHistogramData0.0090.0020.011
calculateJaccard0.0110.0010.012
calculateKappa0.0210.0020.023
calculateSorensenDice0.0070.0000.008
checkInclusion0.0070.0010.009
clustering0.1770.0050.182
deprecated000
distanceDendro0.2220.0080.231
distanceHeatmap0.2020.0110.218
enrichmentWordcloud0.2890.0100.301
fuzzyClustering0.0060.0010.008
getAdjacencyMatrix0.0770.0020.079
getAnnotation114.413 5.022207.616
getBipartiteGraph0.0060.0010.007
getClusterAdjacencyMatrix0.0640.0030.068
getGraphTitle0.0050.0000.006
getId0.1780.0174.851
getInteractionScore0.0390.0250.066
getJaccardMatrix2.5260.0892.642
getKappaMatrix1.0130.1251.151
getMeetMinMatrix5.5730.7086.328
getPPI76.110 1.65478.558
getSorensenDiceMatrix0.5520.0090.563
getStringDB0.1140.0113.091
getpMMMatrix1.0220.0341.063
goDistance5.7870.4836.331
gsHistogram0.1270.0070.135
kMeansClustering0.0140.0060.019
kNN_clustering0.0080.0050.014
louvainClustering0.0640.0070.071
markovClustering0.0780.0050.084
pMMlocal0.0310.0100.041
pamClustering0.0060.0060.013
prepareGenesetData0.0080.0050.013
scaleGO5.7770.4526.292
seedFinding0.0080.0050.013