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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:BgeeDB.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings BgeeDB_2.25.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/BgeeDB.Rcheck’
* using R Under development (unstable) (2023-01-14 r83615)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘BgeeDB/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BgeeDB’ version ‘2.25.0’
* 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 R 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
geneList        14.174  2.384  85.611
deleteLocalData  8.097  5.668  24.866
makeTable       11.011  2.541 152.134
topAnat          6.571  0.289   8.649
formatData       5.108  0.491   9.969
loadTopAnatData  2.792  0.241  34.856
listBgeeSpecies  1.079  0.028   7.500
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  Error in `loadTopAnatData(bgee, stage = "UBERON:0000092")`: File topAnat_GeneToAnatEntities_9913_PRESENCE_UBERON_0000092_RNA_SEQSILVER.tsv is truncated, there may be a temporary problem with the Bgee webservice, or there was an error in the parameters.
  Backtrace:
      ▆
   1. └─BgeeDB::loadTopAnatData(bgee, stage = "UBERON:0000092") at test_loadTopAnatData.R:6:2
  ── Error ('test_topAnat.R:6'): Creating the topAnat object is working ──────────
  Error in `download.file(url = url, destfile = destfile, quiet = quiet)`: download from 'https://bgee.org/bgee15_0/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=ea208dba1e357e82e505fea56ba69592a4052d9eb5aaa3cc6ead6d495cd760e9a04a231b72f0973c765f4db8122f33500731200b04869cabb4f49cc31efd5495&source=BgeeDB_R_package&source_version=2.25.0&data_type=RNA_SEQ&data_qual=SILVER&stage_id=UBERON:0000092' failed
  Backtrace:
      ▆
   1. └─BgeeDB::loadTopAnatData(bgee, stage = "UBERON:0000092") at test_topAnat.R:6:2
   2.   └─BgeeDB:::bgee_download_file(...)
   3.     └─utils::download.file(url = url, destfile = destfile, quiet = quiet)
  
  [ FAIL 2 | WARN 6 | SKIP 0 | PASS 22 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘BgeeDB_Manual.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
  ...
--- re-building ‘BgeeDB_Manual.Rmd’ using rmarkdown
Killed

* checking PDF version of manual ... OK
* DONE

Status: 2 ERRORs
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/BgeeDB.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL BgeeDB
###
##############################################################################
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/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) (2023-01-14 r83615) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (64-bit)

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

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, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, 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 objects are masked from 'package:base':

    I, expand.grid, unname


Loading required package: SparseM

Attaching package: 'SparseM'

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

    backsolve


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_0...

Submitting URL to Bgee webservice... (https://bgee.org/bgee15_0/api/?page=r_package&action=get_all_species&display_type=tsv&source=BgeeDB_R_package&source_version=2.25.0)

Query to Bgee webservice successful!

API key built: ea208dba1e357e82e505fea56ba69592a4052d9eb5aaa3cc6ead6d495cd760e9a04a231b72f0973c765f4db8122f33500731200b04869cabb4f49cc31efd5495

Saved annotation files in /home/biocbuild/bbs-3.17-bioc/meat/BgeeDB.Rcheck/tests/testthat/Mus_musculus_Bgee_15_0 folder.

Extracting expression data matrix...
  Keeping only present genes.

Extracting features information...

Extracting samples information...

Extracting expression data matrix...
  Keeping only present genes.

Extracting features information...

Extracting samples information...

Extracting expression data matrix...
  Keeping only present genes.

Extracting features information...

Extracting samples information...

Querying Bgee to get release information...

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

Submitting URL to Bgee webservice... (https://r.bgee.org/bgee13/?page=species&display_type=tsv&source=BgeeDB_R_package&source_version=2.25.0)

Query to Bgee webservice successful!

API key built: ea208dba1e357e82e505fea56ba69592a4052d9eb5aaa3cc6ead6d495cd760e9a04a231b72f0973c765f4db8122f33500731200b04869cabb4f49cc31efd5495

IMPORTANT INFORMATION: Be careful! You are not using the last release of the Bgee database! If it is not intentional you should update to the last version of Bioconductor and of the BgeeDB package. To update Bioconductor, see https://www.bioconductor.org/install/

Saved annotation files in /home/biocbuild/bbs-3.17-bioc/meat/BgeeDB.Rcheck/tests/testthat/Mus_musculus_Bgee_13_2 folder.

Extracting expression data matrix...
  Keeping only present genes.

Extracting features information...

Extracting samples information...

Extracting expression data matrix...
  Keeping only present genes.

Extracting features information...

Extracting samples information...

Querying Bgee to get release information...

NOTE: the file describing Bgee species information for release 15_0 was found in the download directory /home/biocbuild/bbs-3.17-bioc/meat/BgeeDB.Rcheck/tests/testthat. Data will not be redownloaded.

API key built: ea208dba1e357e82e505fea56ba69592a4052d9eb5aaa3cc6ead6d495cd760e9a04a231b72f0973c765f4db8122f33500731200b04869cabb4f49cc31efd5495

Querying Bgee to get release information...

NOTE: the file describing Bgee species information for release 15_0 was found in the download directory /home/biocbuild/bbs-3.17-bioc/meat/BgeeDB.Rcheck/tests/testthat. Data will not be redownloaded.

API key built: ea208dba1e357e82e505fea56ba69592a4052d9eb5aaa3cc6ead6d495cd760e9a04a231b72f0973c765f4db8122f33500731200b04869cabb4f49cc31efd5495

Saved annotation files in /home/biocbuild/bbs-3.17-bioc/meat/BgeeDB.Rcheck/tests/testthat/Mus_musculus_Bgee_15_0 folder.

Querying Bgee to get release information...

NOTE: the file describing Bgee species information for release 13_2 was found in the download directory /home/biocbuild/bbs-3.17-bioc/meat/BgeeDB.Rcheck/tests/testthat. Data will not be redownloaded.

API key built: ea208dba1e357e82e505fea56ba69592a4052d9eb5aaa3cc6ead6d495cd760e9a04a231b72f0973c765f4db8122f33500731200b04869cabb4f49cc31efd5495

IMPORTANT INFORMATION: Be careful! You are not using the last release of the Bgee database! If it is not intentional you should update to the last version of Bioconductor and of the BgeeDB package. To update Bioconductor, see https://www.bioconductor.org/install/

Querying Bgee to get release information...

NOTE: the file describing Bgee species information for release 13_2 was found in the download directory /home/biocbuild/bbs-3.17-bioc/meat/BgeeDB.Rcheck/tests/testthat. Data will not be redownloaded.

API key built: ea208dba1e357e82e505fea56ba69592a4052d9eb5aaa3cc6ead6d495cd760e9a04a231b72f0973c765f4db8122f33500731200b04869cabb4f49cc31efd5495

IMPORTANT INFORMATION: Be careful! You are not using the last release of the Bgee database! If it is not intentional you should update to the last version of Bioconductor and of the BgeeDB package. To update Bioconductor, see https://www.bioconductor.org/install/

Saved annotation files in /home/biocbuild/bbs-3.17-bioc/meat/BgeeDB.Rcheck/tests/testthat/Mus_musculus_Bgee_13_2 folder.

Querying Bgee to get release information...

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

Submitting URL to Bgee webservice... (https://r.bgee.org/bgee14_2/?page=r_package&action=get_all_species&display_type=tsv&source=BgeeDB_R_package&source_version=2.25.0)

Query to Bgee webservice successful!

Querying Bgee to get release information...

NOTE: the file describing Bgee species information for release 15_0 was found in the download directory /home/biocbuild/bbs-3.17-bioc/meat/BgeeDB.Rcheck/tests/testthat. Data will not be redownloaded.

API key built: ea208dba1e357e82e505fea56ba69592a4052d9eb5aaa3cc6ead6d495cd760e9a04a231b72f0973c765f4db8122f33500731200b04869cabb4f49cc31efd5495

Building URLs to retrieve organ relationships from Bgee.........
   URL successfully built (https://bgee.org/bgee15_0/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=ea208dba1e357e82e505fea56ba69592a4052d9eb5aaa3cc6ead6d495cd760e9a04a231b72f0973c765f4db8122f33500731200b04869cabb4f49cc31efd5495&source=BgeeDB_R_package&source_version=2.25.0)
   Submitting URL to Bgee webservice (can be long)
   Got results from Bgee webservice. Files are written in "/home/biocbuild/bbs-3.17-bioc/meat/BgeeDB.Rcheck/tests/testthat/Bos_taurus_Bgee_15_0"

Building URLs to retrieve organ names from Bgee.................
   URL successfully built (https://bgee.org/bgee15_0/api/?page=r_package&action=get_anat_entities&display_type=tsv&species_list=9913&attr_list=ID&attr_list=NAME&api_key=ea208dba1e357e82e505fea56ba69592a4052d9eb5aaa3cc6ead6d495cd760e9a04a231b72f0973c765f4db8122f33500731200b04869cabb4f49cc31efd5495&source=BgeeDB_R_package&source_version=2.25.0)
   Submitting URL to Bgee webservice (can be long)
   Got results from Bgee webservice. Files are written in "/home/biocbuild/bbs-3.17-bioc/meat/BgeeDB.Rcheck/tests/testthat/Bos_taurus_Bgee_15_0"

Building URLs to retrieve mapping of gene to organs from Bgee...
   URL successfully built (https://bgee.org/bgee15_0/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=ea208dba1e357e82e505fea56ba69592a4052d9eb5aaa3cc6ead6d495cd760e9a04a231b72f0973c765f4db8122f33500731200b04869cabb4f49cc31efd5495&source=BgeeDB_R_package&source_version=2.25.0&data_type=RNA_SEQ&data_qual=SILVER&stage_id=UBERON:0000092)
   Submitting URL to Bgee webservice (can be long)

Querying Bgee to get release information...

NOTE: the file describing Bgee species information for release 15_0 was found in the download directory /home/biocbuild/bbs-3.17-bioc/meat/BgeeDB.Rcheck/tests/testthat. Data will not be redownloaded.

API key built: ea208dba1e357e82e505fea56ba69592a4052d9eb5aaa3cc6ead6d495cd760e9a04a231b72f0973c765f4db8122f33500731200b04869cabb4f49cc31efd5495

Saved annotation files in /home/biocbuild/bbs-3.17-bioc/meat/BgeeDB.Rcheck/tests/testthat/Drosophila_simulans_Bgee_15_0 folder.

Querying Bgee to get release information...

NOTE: the file describing Bgee species information for release 15_0 was found in the download directory /home/biocbuild/bbs-3.17-bioc/meat/BgeeDB.Rcheck/tests/testthat. Data will not be redownloaded.

API key built: ea208dba1e357e82e505fea56ba69592a4052d9eb5aaa3cc6ead6d495cd760e9a04a231b72f0973c765f4db8122f33500731200b04869cabb4f49cc31efd5495

Querying Bgee to get release information...

NOTE: the file describing Bgee species information for release 15_0 was found in the download directory /home/biocbuild/bbs-3.17-bioc/meat/BgeeDB.Rcheck/tests/testthat. Data will not be redownloaded.

API key built: ea208dba1e357e82e505fea56ba69592a4052d9eb5aaa3cc6ead6d495cd760e9a04a231b72f0973c765f4db8122f33500731200b04869cabb4f49cc31efd5495

NOTE: an organ relationships file was found in the download directory /home/biocbuild/bbs-3.17-bioc/meat/BgeeDB.Rcheck/tests/testthat/Bos_taurus_Bgee_15_0. Data will not be redownloaded.

NOTE: an organ names file was found in the download directory /home/biocbuild/bbs-3.17-bioc/meat/BgeeDB.Rcheck/tests/testthat/Bos_taurus_Bgee_15_0. Data will not be redownloaded.

Building URLs to retrieve mapping of gene to organs from Bgee...
   URL successfully built (https://bgee.org/bgee15_0/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=ea208dba1e357e82e505fea56ba69592a4052d9eb5aaa3cc6ead6d495cd760e9a04a231b72f0973c765f4db8122f33500731200b04869cabb4f49cc31efd5495&source=BgeeDB_R_package&source_version=2.25.0&data_type=RNA_SEQ&data_qual=SILVER&stage_id=UBERON:0000092)
   Submitting URL to Bgee webservice (can be long)
[ FAIL 2 | WARN 6 | SKIP 0 | PASS 22 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_loadTopAnatData.R:6'): Loading of topAnatData files is working ──
Error in `loadTopAnatData(bgee, stage = "UBERON:0000092")`: File topAnat_GeneToAnatEntities_9913_PRESENCE_UBERON_0000092_RNA_SEQSILVER.tsv is truncated, there may be a temporary problem with the Bgee webservice, or there was an error in the parameters.
Backtrace:
    ▆
 1. └─BgeeDB::loadTopAnatData(bgee, stage = "UBERON:0000092") at test_loadTopAnatData.R:6:2
── Error ('test_topAnat.R:6'): Creating the topAnat object is working ──────────
Error in `download.file(url = url, destfile = destfile, quiet = quiet)`: download from 'https://bgee.org/bgee15_0/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=ea208dba1e357e82e505fea56ba69592a4052d9eb5aaa3cc6ead6d495cd760e9a04a231b72f0973c765f4db8122f33500731200b04869cabb4f49cc31efd5495&source=BgeeDB_R_package&source_version=2.25.0&data_type=RNA_SEQ&data_qual=SILVER&stage_id=UBERON:0000092' failed
Backtrace:
    ▆
 1. └─BgeeDB::loadTopAnatData(bgee, stage = "UBERON:0000092") at test_topAnat.R:6:2
 2.   └─BgeeDB:::bgee_download_file(...)
 3.     └─utils::download.file(url = url, destfile = destfile, quiet = quiet)

[ FAIL 2 | WARN 6 | SKIP 0 | PASS 22 ]
Error: Test failures
Execution halted