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###
### 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_1.1.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/GeDi.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GeDi/DESCRIPTION’ ... OK
* this is package ‘GeDi’ version ‘1.1.1’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* 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 ... 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
> 
> string_db <- getStringDB(9606)
> string_db
***********  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 68.5 MB

Warning in download.file(urlStr, temp) :
  downloaded length 71843578 != 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': status was 'Transferred a partial file'
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:
   2.   └─BiocNeighbors::findKNN(scores, k, warn.ties = FALSE)
   3.     └─methods (local) `<fn>`(`<list>`, `<nnstndGF>`, `<env>`)
  ── 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.   └─string_db$get_interactions(string_ids)
   3.     └─STRINGdb (local) load()
   4.       └─STRINGdb::downloadAbsentFile(url, oD = input_directory)
   5.         └─utils::download.file(urlStr, temp)
  
  [ FAIL 2 | WARN 2 | SKIP 0 | PASS 180 ]
  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: 2 ERRORs
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/GeDi.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL GeDi
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’
* installing *source* package ‘GeDi’ ...
** 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 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-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 64.2 MB


preparing gene to GO mapping data...
preparing gene to GO mapping data...
[ FAIL 2 | WARN 2 | SKIP 0 | PASS 180 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-clustering.R:143:3'): kNN clustering works correctly ───────────
Error: unable to find an inherited method for function 'findKNN' for signature 'X = "dsyMatrix"'
Backtrace:
    ▆
 1. └─GeDi::kNN_clustering(distances, 3) at test-clustering.R:143:3
 2.   └─BiocNeighbors::findKNN(scores, k, warn.ties = FALSE)
 3.     └─methods (local) `<fn>`(`<list>`, `<nnstndGF>`, `<env>`)
── 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.   └─string_db$get_interactions(string_ids)
 3.     └─STRINGdb (local) load()
 4.       └─STRINGdb::downloadAbsentFile(url, oD = input_directory)
 5.         └─utils::download.file(urlStr, temp)

[ FAIL 2 | WARN 2 | SKIP 0 | PASS 180 ]
Error: Test failures
Execution halted