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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_2.32.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/BgeeDB.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* 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 ‘2.32.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                     user system elapsed
makeTable           9.919  4.527  98.170
geneList           12.937  0.707  72.173
topAnat             4.978  0.470   7.084
getIntegratedCalls  3.468  0.836  20.267
deleteLocalData     3.876  0.396   9.074
formatData          2.487  0.265   6.064
loadTopAnatData     1.669  0.728  30.502
listBgeeSpecies     0.086  0.025   9.812
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: OK

##############################################################################
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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/4.4-x86_64/Resources/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 version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 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

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, saveRDS, setdiff, 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 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: 532fd995d8b2c87d843d3b7bc7cbfed5353803e27961b4933660f46bc22b50f33c076f5d011857975960732ae7157b49e3973618a7c25d0fdcbc4b970fe61bc2

Saved annotation files in /Users/biocbuild/bbs-3.20-bioc/meat/BgeeDB.Rcheck/tests/testthat/Mus_musculus_Bgee_15_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...

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

downloading Bgee species info... (https://r.bgee.org/bgee13/?page=species&display_type=tsv&source=BgeeDB_R_package&source_version=2.32.0)

Download of species information successful!

API key built: 532fd995d8b2c87d843d3b7bc7cbfed5353803e27961b4933660f46bc22b50f33c076f5d011857975960732ae7157b49e3973618a7c25d0fdcbc4b970fe61bc2

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 /Users/biocbuild/bbs-3.20-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_2 was found in the download directory /Users/biocbuild/bbs-3.20-bioc/meat/BgeeDB.Rcheck/tests/testthat. Data will not be redownloaded.

API key built: 532fd995d8b2c87d843d3b7bc7cbfed5353803e27961b4933660f46bc22b50f33c076f5d011857975960732ae7157b49e3973618a7c25d0fdcbc4b970fe61bc2

Querying Bgee to get release information...

NOTE: the file describing Bgee species information for release 15_2 was found in the download directory /Users/biocbuild/bbs-3.20-bioc/meat/BgeeDB.Rcheck/tests/testthat. Data will not be redownloaded.

API key built: 532fd995d8b2c87d843d3b7bc7cbfed5353803e27961b4933660f46bc22b50f33c076f5d011857975960732ae7157b49e3973618a7c25d0fdcbc4b970fe61bc2

Saved annotation files in /Users/biocbuild/bbs-3.20-bioc/meat/BgeeDB.Rcheck/tests/testthat/Mus_musculus_Bgee_15_2 folder.

Querying Bgee to get release information...

NOTE: the file describing Bgee species information for release 13_2 was found in the download directory /Users/biocbuild/bbs-3.20-bioc/meat/BgeeDB.Rcheck/tests/testthat. Data will not be redownloaded.

API key built: 532fd995d8b2c87d843d3b7bc7cbfed5353803e27961b4933660f46bc22b50f33c076f5d011857975960732ae7157b49e3973618a7c25d0fdcbc4b970fe61bc2

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 /Users/biocbuild/bbs-3.20-bioc/meat/BgeeDB.Rcheck/tests/testthat. Data will not be redownloaded.

API key built: 532fd995d8b2c87d843d3b7bc7cbfed5353803e27961b4933660f46bc22b50f33c076f5d011857975960732ae7157b49e3973618a7c25d0fdcbc4b970fe61bc2

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 /Users/biocbuild/bbs-3.20-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...

downloading Bgee species info... (https://r.bgee.org/bgee14_2/?page=r_package&action=get_all_species&display_type=tsv&source=BgeeDB_R_package&source_version=2.32.0)

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 /Users/biocbuild/bbs-3.20-bioc/meat/BgeeDB.Rcheck/tests/testthat. Data will not be redownloaded.

API key built: 532fd995d8b2c87d843d3b7bc7cbfed5353803e27961b4933660f46bc22b50f33c076f5d011857975960732ae7157b49e3973618a7c25d0fdcbc4b970fe61bc2

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=532fd995d8b2c87d843d3b7bc7cbfed5353803e27961b4933660f46bc22b50f33c076f5d011857975960732ae7157b49e3973618a7c25d0fdcbc4b970fe61bc2&source=BgeeDB_R_package&source_version=2.32.0)
   Submitting URL to Bgee webservice (can be long)
   Got results from Bgee webservice. Files are written in "/Users/biocbuild/bbs-3.20-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=532fd995d8b2c87d843d3b7bc7cbfed5353803e27961b4933660f46bc22b50f33c076f5d011857975960732ae7157b49e3973618a7c25d0fdcbc4b970fe61bc2&source=BgeeDB_R_package&source_version=2.32.0)
   Submitting URL to Bgee webservice (can be long)
   Got results from Bgee webservice. Files are written in "/Users/biocbuild/bbs-3.20-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=532fd995d8b2c87d843d3b7bc7cbfed5353803e27961b4933660f46bc22b50f33c076f5d011857975960732ae7157b49e3973618a7c25d0fdcbc4b970fe61bc2&source=BgeeDB_R_package&source_version=2.32.0&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 "/Users/biocbuild/bbs-3.20-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 /Users/biocbuild/bbs-3.20-bioc/meat/BgeeDB.Rcheck/tests/testthat. Data will not be redownloaded.

API key built: 532fd995d8b2c87d843d3b7bc7cbfed5353803e27961b4933660f46bc22b50f33c076f5d011857975960732ae7157b49e3973618a7c25d0fdcbc4b970fe61bc2

Saved annotation files in /Users/biocbuild/bbs-3.20-bioc/meat/BgeeDB.Rcheck/tests/testthat/Drosophila_simulans_Bgee_15_2 folder.

Querying Bgee to get release information...

NOTE: the file describing Bgee species information for release 15_2 was found in the download directory /Users/biocbuild/bbs-3.20-bioc/meat/BgeeDB.Rcheck/tests/testthat. Data will not be redownloaded.

API key built: 532fd995d8b2c87d843d3b7bc7cbfed5353803e27961b4933660f46bc22b50f33c076f5d011857975960732ae7157b49e3973618a7c25d0fdcbc4b970fe61bc2

Querying Bgee to get release information...

NOTE: the file describing Bgee species information for release 15_2 was found in the download directory /Users/biocbuild/bbs-3.20-bioc/meat/BgeeDB.Rcheck/tests/testthat. Data will not be redownloaded.

API key built: 532fd995d8b2c87d843d3b7bc7cbfed5353803e27961b4933660f46bc22b50f33c076f5d011857975960732ae7157b49e3973618a7c25d0fdcbc4b970fe61bc2

NOTE: an organ relationships file was found in the download directory /Users/biocbuild/bbs-3.20-bioc/meat/BgeeDB.Rcheck/tests/testthat/Bos_taurus_Bgee_15_2. Data will not be redownloaded.

NOTE: an organ names file was found in the download directory /Users/biocbuild/bbs-3.20-bioc/meat/BgeeDB.Rcheck/tests/testthat/Bos_taurus_Bgee_15_2. Data will not be redownloaded.

NOTE: a gene to organs mapping file was found in the download directory /Users/biocbuild/bbs-3.20-bioc/meat/BgeeDB.Rcheck/tests/testthat/Bos_taurus_Bgee_15_2. Data will not be redownloaded.

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

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

Done.

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. 98 genes in background will be kept.

Building most specific Ontology terms...  (  110  Ontology terms found. )

Building DAG topology...................  (  549  Ontology terms and  994  relations. )

Annotating nodes (Can be long)..........  (  95  genes annotated to the Ontology terms. )
[ FAIL 0 | WARN 8 | SKIP 0 | PASS 32 ]

[ FAIL 0 | WARN 8 | SKIP 0 | PASS 32 ]
> 
> proc.time()
   user  system elapsed 
 32.803   3.201 134.575