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### 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_1.6.0.tar.gz
###
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* 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 ‘1.6.0’
* 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 103.054  5.943 325.647
getPPI         73.522  1.669  76.225
scaleGO         7.958  0.256   8.226
goDistance      7.299  0.403   7.716
getId           0.162  0.021  12.517
getStringDB     0.164  0.016  69.649
* 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 ════════════════════════════════════════════════════════════════
  ── 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
  In addition: 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 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
  ‘/home/biocbuild/bbs-3.22-bioc/meat/GeDi.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL GeDi
###
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* installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’
* installing *source* package ‘GeDi’ ...
** this is package ‘GeDi’ version ‘1.6.0’
** 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)

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