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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_2.32.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/BgeeDB.Rcheck’
* using R version 4.4.1 (2024-06-14)
* 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 ‘2.32.0’
* 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", "sc_droplet_based") for the next steps.

Querying Bgee to get release information...

NOTE: the file describing Bgee species information for release 15_2 was found in the download directory /home/biocbuild/bbs-3.20-bioc/meat/BgeeDB.Rcheck. Data will not be redownloaded.

API key built: 2316e474acf2f8a5d57b5f39c98d5081a1dde364c658f057d93891ae66d0a3d7db7ddce3797eb488c0e419d5ede59804848f242a6bae6c4d296b3ab0d30f6fa4
> myTopAnatData <- loadTopAnatData(bgee)

Building URLs to retrieve organ relationships from Bgee.........
   URL successfully built (https://www.bgee.org/bgee15_2/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=2316e474acf2f8a5d57b5f39c98d5081a1dde364c658f057d93891ae66d0a3d7db7ddce3797eb488c0e419d5ede59804848f242a6bae6c4d296b3ab0d30f6fa4&source=BgeeDB_R_package&source_version=2.32.0)
   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_2"

Building URLs to retrieve organ names from Bgee.................
   URL successfully built (https://www.bgee.org/bgee15_2/api/?page=r_package&action=get_anat_entities&display_type=tsv&species_list=7955&attr_list=ID&attr_list=NAME&api_key=2316e474acf2f8a5d57b5f39c98d5081a1dde364c658f057d93891ae66d0a3d7db7ddce3797eb488c0e419d5ede59804848f242a6bae6c4d296b3ab0d30f6fa4&source=BgeeDB_R_package&source_version=2.32.0)
   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_2"

Building URLs to retrieve mapping of gene to organs from Bgee...
   URL successfully built (https://www.bgee.org/bgee15_2/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=2316e474acf2f8a5d57b5f39c98d5081a1dde364c658f057d93891ae66d0a3d7db7ddce3797eb488c0e419d5ede59804848f242a6bae6c4d296b3ab0d30f6fa4&source=BgeeDB_R_package&source_version=2.32.0&data_qual=SILVER)
   Submitting URL to Bgee webservice (can be long)
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* 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
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/BgeeDB.Rcheck/00check.log’
for details.