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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_2.35.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/BgeeDB.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 ‘BgeeDB/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BgeeDB’ version ‘2.35.1’
* 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 ‘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 ... NOTE
getDescendant: no visible binding for global variable ‘myBgeeObject’
Undefined global functions or variables:
  myBgeeObject
* 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-3.22-bioc/meat/BgeeDB.Rcheck. Data will not be redownloaded.

API key built: 045aed2950c82a8180b23275474b8f50f94720d2b653f4893b6da9d5072d92552eb01c2edab35a61947d73c6811ef3e5f7fa1627d57194c5162a9ad417f7d07c
> 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=045aed2950c82a8180b23275474b8f50f94720d2b653f4893b6da9d5072d92552eb01c2edab35a61947d73c6811ef3e5f7fa1627d57194c5162a9ad417f7d07c&source=BgeeDB_R_package&source_version=2.35.1)
   Submitting URL to Bgee webservice (can be long)
   Got results from Bgee webservice. Files are written in "/home/biocbuild/bbs-3.22-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=045aed2950c82a8180b23275474b8f50f94720d2b653f4893b6da9d5072d92552eb01c2edab35a61947d73c6811ef3e5f7fa1627d57194c5162a9ad417f7d07c&source=BgeeDB_R_package&source_version=2.35.1)
   Submitting URL to Bgee webservice (can be long)
   Got results from Bgee webservice. Files are written in "/home/biocbuild/bbs-3.22-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=045aed2950c82a8180b23275474b8f50f94720d2b653f4893b6da9d5072d92552eb01c2edab35a61947d73c6811ef3e5f7fa1627d57194c5162a9ad417f7d07c&source=BgeeDB_R_package&source_version=2.35.1&data_qual=SILVER)
   Submitting URL to Bgee webservice (can be long)
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
deleteLocalData 3.430  0.500 103.331
formatData      2.962  0.373   7.368
Bgee-class      0.101  0.008   7.252
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’

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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL BgeeDB
###
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* installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’
* installing *source* package ‘BgeeDB’ ...
** this is package ‘BgeeDB’ version ‘2.35.1’
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading

groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location

groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.
** testing if installed package can be loaded from final location

groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.
** testing if installed package keeps a record of temporary installation path
* DONE (BgeeDB)

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(BgeeDB)
Loading required package: topGO
Loading required package: BiocGenerics
Loading required package: generics

Attaching package: 'generics'

The following objects are masked from 'package:base':

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union