Multiple platform build/check report for BioC 3.23 - CHECK results for GeDi on nebbiolo1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.3 LTS)	x86_64	R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences"	4869
kjohnson3	macOS 13.7.7 Ventura	arm64	R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences"	4576
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*

CHECK results for GeDi on nebbiolo1

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: 1.7.1

Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:GeDi.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings GeDi_1.7.1.tar.gz

StartedAt: 2025-12-04 01:42:15 -0500 (Thu, 04 Dec 2025)

EndedAt: 2025-12-04 02:10:10 -0500 (Thu, 04 Dec 2025)

EllapsedTime: 1675.1 seconds

RetCode: 1

Status: ERROR

CheckDir: GeDi.Rcheck

Warnings: NA

Command output

##############################################################################
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### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:GeDi.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings GeDi_1.7.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/GeDi.Rcheck’
* using R Under development (unstable) (2025-10-20 r88955)
* 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 ‘1.7.1’
* 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 ... ERROR
Running examples in ‘GeDi-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: getAnnotation
> ### Title: Get the annotation of a 'STRINGdb' object
> ### Aliases: getAnnotation
> 
> ### ** Examples
> 
> stringdb <- getStringDB(9606)
> stringdb
***********  STRING - https://string-db.org   ***********
(Search Tool for the Retrieval of Interacting Genes/Proteins)  
version: 12.0
species: 9606
............please wait............
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 40.9 MB

Warning in download.file(urlStr, temp) :
  downloaded length 42893050 != reported length 83164437
Warning in download.file(urlStr, temp) :
  URL 'https://stringdb-downloads.org/download/protein.links.v12.0/9606.protein.links.v12.0.txt.gz': Timeout of 600 seconds was reached
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
Calls: <Anonymous> ... get_graph -> load -> downloadAbsentFile -> download.file
Execution halted
* 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:
  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.
  Warning message:
  In for (i in seq_len(n)) { : closing unused connection 4 ()
  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: 2 ERRORs
See
  ‘/home/biocbuild/bbs-3.23-bioc/meat/GeDi.Rcheck/00check.log’
for details.

Installation output

GeDi.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL GeDi
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’
* installing *source* package ‘GeDi’ ...
** this is package ‘GeDi’ version ‘1.7.1’
** 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)

Tests output

GeDi.Rcheck/tests/testthat.Rout.fail


R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences"
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 39.0 MB

Saving _problems/test-downloadPPI-28.R

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.
Warning message:
In for (i in seq_len(n)) { : closing unused connection 4 ()
Execution halted

Example timings

GeDi.Rcheck/GeDi-Ex.timings

name	user	system	elapsed
GeDi	0.007	0.000	0.007
buildClusterGraph	0.094	0.004	0.097
buildGraph	0.058	0.001	0.059
buildHistogramData	0.008	0.000	0.008
checkInclusion	0.007	0.001	0.008
clustering	0.108	0.002	0.110
deprecated	0	0	0
distanceDendro	0.152	0.005	0.157
distanceHeatmap	0.129	0.001	0.130
dot-cluster_markov	0.532	0.004	0.536
dot-map_to_color	0.013	0.010	0.023
enrichmentWordcloud	0.227	0.011	0.237
fuzzyClustering	0.008	0.000	0.007
getAdjacencyMatrix	0.063	0.012	0.075