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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BgeeDB.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BgeeDB_2.34.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/BgeeDB.Rcheck’
* using R version 4.5.1 RC (2025-06-05 r88288)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* 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 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: listBgeeSpecies
> ### Title: List species in the Bgee database and the available data types
> ###   for each of them
> ### Aliases: listBgeeSpecies
> 
> ### ** Examples
> 
> {
+  listBgeeSpecies()
+  # species present in a specific Bgee release
+  listBgeeSpecies(release = "13.2")
+  # in order to order species according to theit taxonomical IDs
+  listBgeeSpecies(ordering = 1)
+ }

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!

Querying Bgee to get release information...

Building URL to query species in Bgee release 13_2...

downloading Bgee species info... (https://archives.bgee.org/13-2/?page=species&display_type=tsv&source=BgeeDB_R_package&source_version=2.34.0)

Download of species information successful!

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)
Warning in download.file(url = url, destfile = destfile, quiet = quiet) :
  URL 'https://www.bgee.org/ftp/bgee_v15_2/rPackageSpeciesInfo.tsv': status was 'SSL connect error'
Error in download.file(url = url, destfile = destfile, quiet = quiet) : 
  cannot open URL 'https://www.bgee.org/ftp/bgee_v15_2/rPackageSpeciesInfo.tsv'
Calls: listBgeeSpecies -> bgee_download_file -> download.file
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
                         user system elapsed
geneList               20.119  1.063 358.755
formatData              6.453  3.461 301.746
deleteLocalData         7.231  0.843 129.860
getIntegratedCalls      5.916  0.988 107.439
getData                 1.896  0.197  68.471
getSampleProcessedData  1.758  0.164 107.241
Bgee-class              0.151  0.052 132.504
getAnnotation           0.095  0.027  42.941
deleteOldData           0.053  0.022  75.747
listBgeeRelease         0.048  0.022  56.426
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL BgeeDB
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/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 version 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-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(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...
Error in download.file(url = url, destfile = destfile, quiet = quiet) : 
  cannot open URL 'https://www.bgee.org/ftp/release_v2.tsv'

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'

Querying Bgee to get release information...