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###
### Running command:
###
###   /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_2.34.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/BgeeDB.Rcheck’
* using R Under development (unstable) (2025-02-19 r87757)
* 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-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 ‘2.34.0’
* 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: deleteLocalData
> ### Title: Delete local data for the species of the reference class Bgee
> ###   object
> ### Aliases: deleteLocalData
> 
> ### ** Examples
> 
> {
+   bgee <- Bgee$new(species = "Mus_musculus", dataType = "rna_seq")
+   data <- getData(bgee, experimentId = "SRP007359")
+   deleteLocalData(bgee, allDataTypes = TRUE)
+ }

Querying Bgee to get release information...
Warning in download.file(url = url, destfile = destfile, quiet = quiet) :
  URL 'https://www.bgee.org/ftp/release_v2.tsv': status was 'SSL connect error'
Error in download.file(url = url, destfile = destfile, quiet = quiet) : 
  cannot open URL 'https://www.bgee.org/ftp/release_v2.tsv'
Warning in file.remove(file.path(getwd(), "release.tsv.tmp")) :
  cannot remove file '/home/biocbuild/bbs-3.21-bioc/meat/BgeeDB.Rcheck/release.tsv.tmp', reason 'No such file or directory'

WARNING: BgeeDB could not access Bgee releases information from the internet, but a release information file was found in the download directory /home/biocbuild/bbs-3.21-bioc/meat/BgeeDB.Rcheck. This release file will be used, but be warned that it may not be up to date!

NOTE: the file describing Bgee species information for release 15_2 was found in the download directory /home/biocbuild/bbs-3.21-bioc/meat/BgeeDB.Rcheck. Data will not be redownloaded.

API key built: 54b04cb6cccae0b35e6788b7ef3971e125740041754e50dac509bab213026da907059c0c15ac975adcfd0afb4ab9822c45e423abe2027245b6c99945f47d3407
Warning in getData(bgee, experimentId = "SRP007359") :
  'getData' is deprecated.
Use 'getSampleProcessedData' instead.
See help("Deprecated")
Examples with CPU (user + system) or elapsed time > 5s
            user system elapsed
Bgee-class 0.124  0.029 125.846
* 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-devel_2025-02-19/site-library’
* installing *source* package ‘BgeeDB’ ...
** this is package ‘BgeeDB’ version ‘2.34.0’
** 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 Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"
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


Attaching package: 'BiocGenerics'

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

    IQR, mad, sd, var, xtabs

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

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
    unsplit, which.max, which.min

Loading required package: graph
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: GO.db
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:utils':

    findMatches

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

    I, expand.grid, unname


Loading required package: SparseM

groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.

Attaching package: 'topGO'

The following object is masked from 'package:IRanges':

    members

Loading required package: tidyr

Attaching package: 'tidyr'

The following object is masked from 'package:S4Vectors':

    expand

The following object is masked from 'package:testthat':

    matches

> 
> Sys.setenv("R_TESTS" = "")
> test_check("BgeeDB")

Querying Bgee to get release information...

Building URL to query species in Bgee release 15_2...

downloading Bgee species info... (https://www.bgee.org/ftp/bgee_v15_2/rPackageSpeciesInfo.tsv)

Download of species information successful!

API key built: 54b04cb6cccae0b35e6788b7ef3971e125740041754e50dac509bab213026da907059c0c15ac975adcfd0afb4ab9822c45e423abe2027245b6c99945f47d3407

Querying Bgee to get release information...
Error in download.file(url = url, destfile = destfile, quiet = quiet) : 
  cannot open URL 'https://www.bgee.org/ftp/release_v2.tsv'

WARNING: BgeeDB could not access Bgee releases information from the internet, but a release information file was found in the download directory /home/biocbuild/bbs-3.21-bioc/meat/BgeeDB.Rcheck/tests/testthat. This release file will be used, but be warned that it may not be up to date!

NOTE: the file describing Bgee species information for release 15_2 was found in the download directory /home/biocbuild/bbs-3.21-bioc/meat/BgeeDB.Rcheck/tests/testthat. Data will not be redownloaded.

API key built: 54b04cb6cccae0b35e6788b7ef3971e125740041754e50dac509bab213026da907059c0c15ac975adcfd0afb4ab9822c45e423abe2027245b6c99945f47d3407

Querying Bgee to get release information...

Building URL to query species in Bgee release 14_2...

downloading Bgee species info... (https://archives.bgee.org/14-2/?page=r_package&action=get_all_species&display_type=tsv&source=BgeeDB_R_package&source_version=2.34.0)

Download of species information successful!

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-3.21-bioc/meat/BgeeDB.Rcheck/tests/testthat. Data will not be redownloaded.

API key built: 54b04cb6cccae0b35e6788b7ef3971e125740041754e50dac509bab213026da907059c0c15ac975adcfd0afb4ab9822c45e423abe2027245b6c99945f47d3407

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=9913&attr_list=SOURCE_ID&attr_list=TARGET_ID&api_key=54b04cb6cccae0b35e6788b7ef3971e125740041754e50dac509bab213026da907059c0c15ac975adcfd0afb4ab9822c45e423abe2027245b6c99945f47d3407&source=BgeeDB_R_package&source_version=2.34.0)
   Submitting URL to Bgee webservice (can be long)
   Got results from Bgee webservice. Files are written in "/home/biocbuild/bbs-3.21-bioc/meat/BgeeDB.Rcheck/tests/testthat/Bos_taurus_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=9913&attr_list=ID&attr_list=NAME&api_key=54b04cb6cccae0b35e6788b7ef3971e125740041754e50dac509bab213026da907059c0c15ac975adcfd0afb4ab9822c45e423abe2027245b6c99945f47d3407&source=BgeeDB_R_package&source_version=2.34.0)
   Submitting URL to Bgee webservice (can be long)
   Got results from Bgee webservice. Files are written in "/home/biocbuild/bbs-3.21-bioc/meat/BgeeDB.Rcheck/tests/testthat/Bos_taurus_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=9913&attr_list=GENE_ID&attr_list=ANAT_ENTITY_ID&api_key=54b04cb6cccae0b35e6788b7ef3971e125740041754e50dac509bab213026da907059c0c15ac975adcfd0afb4ab9822c45e423abe2027245b6c99945f47d3407&source=BgeeDB_R_package&source_version=2.34.0&data_type=RNA_SEQ&data_qual=SILVER&stage_id=UBERON:0000092)
   Submitting URL to Bgee webservice (can be long)
   Got results from Bgee webservice. Files are written in "/home/biocbuild/bbs-3.21-bioc/meat/BgeeDB.Rcheck/tests/testthat/Bos_taurus_Bgee_15_2"

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

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

Done.

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-3.21-bioc/meat/BgeeDB.Rcheck/tests/testthat. Data will not be redownloaded.

API key built: 54b04cb6cccae0b35e6788b7ef3971e125740041754e50dac509bab213026da907059c0c15ac975adcfd0afb4ab9822c45e423abe2027245b6c99945f47d3407

Saved annotation files in /home/biocbuild/bbs-3.21-bioc/meat/BgeeDB.Rcheck/tests/testthat/Drosophila_simulans_Bgee_15_2 folder.

Querying Bgee to get release information...