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### Running command:
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###   /home/biocbuild/R/R/bin/R CMD check --install=check:BgeeDB.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings BgeeDB_2.31.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/BgeeDB.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14)
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BgeeDB/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BgeeDB’ version ‘2.31.0’
* 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 ‘BgeeDB’ 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 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 ‘BgeeDB-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: geneList
> ### Title: Example of gene list object used to run a topAnat enrichment
> ###   test, created on June 2018. The format of the gene list is the same
> ###   as the gene list required to build a 'topGOdata' object in the
> ###   'topGO' package: a vector with background genes as names, and 0 or 1
> ###   values depending if a gene is in the foreground or not. In this
> ###   example the foreground genes are zebrafish genes with an annotated
> ###   phenotype related to "pectoral fin", and the background is composed
> ###   of all zebrafish Ensembl genes with an annotated phenotype from ZFIN.
> ###   The gene list was built using the biomaRt package, and the code used
> ###   can be found in the vignette of the package.
> ### Aliases: geneList
> ### Keywords: datasets
> 
> ### ** Examples
> 
> bgee <- Bgee$new(species = "Danio_rerio")

NOTE: You did not specify any data type. The argument dataType will be set to c("rna_seq","affymetrix","est","in_situ","sc_full_length") for the next steps.

Querying Bgee to get release information...

NOTE: the file describing Bgee species information for release 15_0 was found in the download directory /home/biocbuild/bbs-3.20-bioc/meat/BgeeDB.Rcheck. Data will not be redownloaded.

API key built: f8b0ed8fd21ac69942a18eec8a17e52834d02e9b72f1a2adc934eb1cfb7c60765b921e225883f3f2829955104bb5f9a376be9fe88a755a630495427c2603ca16
> myTopAnatData <- loadTopAnatData(bgee)

Building URLs to retrieve organ relationships from Bgee.........
   URL successfully built (https://www.bgee.org/bgee15_0/api/?page=r_package&action=get_anat_entity_relations&display_type=tsv&species_list=7955&attr_list=SOURCE_ID&attr_list=TARGET_ID&api_key=f8b0ed8fd21ac69942a18eec8a17e52834d02e9b72f1a2adc934eb1cfb7c60765b921e225883f3f2829955104bb5f9a376be9fe88a755a630495427c2603ca16&source=BgeeDB_R_package&source_version=2.31.0)
   Submitting URL to Bgee webservice (can be long)
   Got results from Bgee webservice. Files are written in "/home/biocbuild/bbs-3.20-bioc/meat/BgeeDB.Rcheck/Danio_rerio_Bgee_15_0"

Building URLs to retrieve organ names from Bgee.................
   URL successfully built (https://www.bgee.org/bgee15_0/api/?page=r_package&action=get_anat_entities&display_type=tsv&species_list=7955&attr_list=ID&attr_list=NAME&api_key=f8b0ed8fd21ac69942a18eec8a17e52834d02e9b72f1a2adc934eb1cfb7c60765b921e225883f3f2829955104bb5f9a376be9fe88a755a630495427c2603ca16&source=BgeeDB_R_package&source_version=2.31.0)
   Submitting URL to Bgee webservice (can be long)
   Got results from Bgee webservice. Files are written in "/home/biocbuild/bbs-3.20-bioc/meat/BgeeDB.Rcheck/Danio_rerio_Bgee_15_0"

Building URLs to retrieve mapping of gene to organs from Bgee...
   URL successfully built (https://www.bgee.org/bgee15_0/api/?page=r_package&action=get_expression_calls&display_type=tsv&species_list=7955&attr_list=GENE_ID&attr_list=ANAT_ENTITY_ID&api_key=f8b0ed8fd21ac69942a18eec8a17e52834d02e9b72f1a2adc934eb1cfb7c60765b921e225883f3f2829955104bb5f9a376be9fe88a755a630495427c2603ca16&source=BgeeDB_R_package&source_version=2.31.0&data_qual=SILVER)
   Submitting URL to Bgee webservice (can be long)
   Got results from Bgee webservice. Files are written in "/home/biocbuild/bbs-3.20-bioc/meat/BgeeDB.Rcheck/Danio_rerio_Bgee_15_0"

Parsing the results.............................................

Adding BGEE:0 as unique root of all terms of the ontology.......

Done.
> data(geneList)
> myTopAnatObject <-  topAnat(myTopAnatData, geneList)

Checking topAnatData object.............

Checking gene list......................

WARNING: Some genes in your gene list have no expression data in Bgee, and will not be included in the analysis. 2959 genes in background will be kept.

Building most specific Ontology terms...  (  1316  Ontology terms found. )

Building DAG topology................... 
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’/home/biocbuild/R/R-4.4.0/bin/BATCH: line 60: 800345 Killed                  ${R_HOME}/bin/R -f ${in} ${opts} ${R_BATCH_OPTIONS} > ${out} 2>&1

 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  
  Extracting samples information...
  
  Extracting expression data matrix...
    Keeping only present genes.
  
  Extracting features information...
  
  Extracting samples information...
  
  Querying Bgee to get release information...
  
  Building URL to query species in Bgee release 13_2...
  
  Submitting URL to Bgee webservice... (https://r.bgee.org/bgee13/?page=species&display_type=tsv&source=BgeeDB_R_package&source_version=2.31.0)
* 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
  ‘/home/biocbuild/bbs-3.20-bioc/meat/BgeeDB.Rcheck/00check.log’
for details.