##############################################################################
##############################################################################
###
### 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_2.33.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/BgeeDB.Rcheck’
* using R Under development (unstable) (2024-11-24 r87369)
* 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 ‘2.33.0’
* 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-3.21-bioc/meat/BgeeDB.Rcheck. Data will not be redownloaded.

API key built: cac8d6c96ccacca3f7357eb0673f3007860d20c17a0246ab1f7bf997a9185706c1bc9a49d42a8c7f9b6f1af5f378de4cc50980d71c16800a2e631b2fc78ea9e3
> 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=cac8d6c96ccacca3f7357eb0673f3007860d20c17a0246ab1f7bf997a9185706c1bc9a49d42a8c7f9b6f1af5f378de4cc50980d71c16800a2e631b2fc78ea9e3&source=BgeeDB_R_package&source_version=2.33.0)
   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/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=cac8d6c96ccacca3f7357eb0673f3007860d20c17a0246ab1f7bf997a9185706c1bc9a49d42a8c7f9b6f1af5f378de4cc50980d71c16800a2e631b2fc78ea9e3&source=BgeeDB_R_package&source_version=2.33.0)
   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/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=cac8d6c96ccacca3f7357eb0673f3007860d20c17a0246ab1f7bf997a9185706c1bc9a49d42a8c7f9b6f1af5f378de4cc50980d71c16800a2e631b2fc78ea9e3&source=BgeeDB_R_package&source_version=2.33.0&data_qual=SILVER)
   Submitting URL to Bgee webservice (can be long)
   Got results from Bgee webservice. Files are written in "/home/biocbuild/bbs-3.21-bioc/meat/BgeeDB.Rcheck/Danio_rerio_Bgee_15_2"

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...................  (  2262  Ontology terms and  4630  relations. )

Annotating nodes (Can be long)..........  (  2959  genes annotated to the Ontology terms. )
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
deleteLocalData 3.731  0.355  14.706
formatData      2.538  0.150  19.823
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL BgeeDB
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library’
* installing *source* package ‘BgeeDB’ ...
** 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) (2024-11-24 r87369) -- "Unsuffered Consequences"
Copyright (C) 2024 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