##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:BgeeDB.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings BgeeDB_2.21.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/BgeeDB.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'BgeeDB/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'BgeeDB' version '2.21.3'
* 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 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 ... WARNING
Codoc mismatches from documentation object 'deleteLocalData':
deleteLocalData
  Code: function(myBgeeObject, allDataTypes = FALSE)
  Docs: function(myBgeeObject)
  Argument names in code not in docs:
    allDataTypes

* 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 database for the species of the reference class
> ###   Bgee object
> ### Aliases: deleteLocalData
> 
> ### ** Examples
> 
> {
+   bgee <- Bgee$new(species = "Mus_musculus", dataType = "rna_seq")
+   deleteLocalData(bgee)
+ }

Querying Bgee to get release information...

NOTE: the file describing Bgee species information for release 14_2 was found in the download directory D:/biocbuild/bbs-3.15-bioc/meat/BgeeDB.Rcheck. Data will not be redownloaded.

API key built: b7b4efc57a03bfa7d886b89ba582d181707f17f0c2ed3af43b29abd94bedbb15fb03720f65700e1ad3de35052bdebe3e7fe2f2c095d295c16e29eb9333832e7f
Error: no such table: rna_seq
Execution halted
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'testthat.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 1 WARNING
See
  'D:/biocbuild/bbs-3.15-bioc/meat/BgeeDB.Rcheck/00check.log'
for details.

##############################################################################
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###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL BgeeDB
###
##############################################################################
##############################################################################


* installing to library 'D:/biocbuild/bbs-3.15-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
  converting help for package 'BgeeDB'
    finding HTML links ... done
    Bgee-class                              html  
    deleteLocalData                         html  
    deleteOldData                           html  
    formatData                              html  
    geneList                                html  
    getAnnotation                           html  
    getData                                 html  
    listBgeeRelease                         html  
    listBgeeSpecies                         html  
    loadTopAnatData                         html  
    makeTable                               html  
    topAnat                                 html  
** 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)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'microbiomeExplorer' is missing or broken
Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'RNAinteract' is missing or broken
 done

R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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, 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


Attaching package: 'IRanges'

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

    windows


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 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=2.21.3)

Query to Bgee webservice successful!

API key built: b7b4efc57a03bfa7d886b89ba582d181707f17f0c2ed3af43b29abd94bedbb15fb03720f65700e1ad3de35052bdebe3e7fe2f2c095d295c16e29eb9333832e7f

Saved annotation files in D:/biocbuild/bbs-3.15-bioc/meat/BgeeDB.Rcheck/tests/testthat/Mus_musculus_Bgee_14_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...

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=2.21.3)

Query to Bgee webservice successful!

API key built: b7b4efc57a03bfa7d886b89ba582d181707f17f0c2ed3af43b29abd94bedbb15fb03720f65700e1ad3de35052bdebe3e7fe2f2c095d295c16e29eb9333832e7f

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 D:/biocbuild/bbs-3.15-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 14_2 was found in the download directory D:/biocbuild/bbs-3.15-bioc/meat/BgeeDB.Rcheck/tests/testthat. Data will not be redownloaded.

API key built: b7b4efc57a03bfa7d886b89ba582d181707f17f0c2ed3af43b29abd94bedbb15fb03720f65700e1ad3de35052bdebe3e7fe2f2c095d295c16e29eb9333832e7f

NOTE: annotation files for this species were found in the download directory D:/biocbuild/bbs-3.15-bioc/meat/BgeeDB.Rcheck/tests/testthat/Mus_musculus_Bgee_14_2. Data will not be redownloaded.

Querying Bgee to get release information...

NOTE: the file describing Bgee species information for release 14_2 was found in the download directory D:/biocbuild/bbs-3.15-bioc/meat/BgeeDB.Rcheck/tests/testthat. Data will not be redownloaded.

API key built: b7b4efc57a03bfa7d886b89ba582d181707f17f0c2ed3af43b29abd94bedbb15fb03720f65700e1ad3de35052bdebe3e7fe2f2c095d295c16e29eb9333832e7f

Saved annotation files in D:/biocbuild/bbs-3.15-bioc/meat/BgeeDB.Rcheck/tests/testthat/Mus_musculus_Bgee_14_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 D:/biocbuild/bbs-3.15-bioc/meat/BgeeDB.Rcheck/tests/testthat. Data will not be redownloaded.

API key built: b7b4efc57a03bfa7d886b89ba582d181707f17f0c2ed3af43b29abd94bedbb15fb03720f65700e1ad3de35052bdebe3e7fe2f2c095d295c16e29eb9333832e7f

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/

NOTE: annotation files for this species were found in the download directory D:/biocbuild/bbs-3.15-bioc/meat/BgeeDB.Rcheck/tests/testthat/Mus_musculus_Bgee_13_2. Data will not be redownloaded.

Querying Bgee to get release information...

NOTE: the file describing Bgee species information for release 13_2 was found in the download directory D:/biocbuild/bbs-3.15-bioc/meat/BgeeDB.Rcheck/tests/testthat. Data will not be redownloaded.

API key built: b7b4efc57a03bfa7d886b89ba582d181707f17f0c2ed3af43b29abd94bedbb15fb03720f65700e1ad3de35052bdebe3e7fe2f2c095d295c16e29eb9333832e7f

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 D:/biocbuild/bbs-3.15-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=2.21.3)

Query to Bgee webservice successful!

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=2.21.3)

Query to Bgee webservice successful!

API key built: b7b4efc57a03bfa7d886b89ba582d181707f17f0c2ed3af43b29abd94bedbb15fb03720f65700e1ad3de35052bdebe3e7fe2f2c095d295c16e29eb9333832e7f

Building URLs to retrieve organ relationships from Bgee.........
   URL successfully built (https://r.bgee.org/bgee14_2/?page=r_package&action=get_anat_entity_relations&display_type=tsv&species_list=9913&attr_list=SOURCE_ID&attr_list=TARGET_ID&api_key=b7b4efc57a03bfa7d886b89ba582d181707f17f0c2ed3af43b29abd94bedbb15fb03720f65700e1ad3de35052bdebe3e7fe2f2c095d295c16e29eb9333832e7f&source=BgeeDB_R_package&source_version=2.21.3)
   Submitting URL to Bgee webservice (can be long)
   Got results from Bgee webservice. Files are written in "D:/biocbuild/bbs-3.15-bioc/meat/BgeeDB.Rcheck/tests/testthat/Bos_taurus_Bgee_14_2"

Building URLs to retrieve organ names from Bgee.................
   URL successfully built (https://r.bgee.org/bgee14_2/?page=r_package&action=get_anat_entities&display_type=tsv&species_list=9913&attr_list=ID&attr_list=NAME&api_key=b7b4efc57a03bfa7d886b89ba582d181707f17f0c2ed3af43b29abd94bedbb15fb03720f65700e1ad3de35052bdebe3e7fe2f2c095d295c16e29eb9333832e7f&source=BgeeDB_R_package&source_version=2.21.3)
   Submitting URL to Bgee webservice (can be long)
   Got results from Bgee webservice. Files are written in "D:/biocbuild/bbs-3.15-bioc/meat/BgeeDB.Rcheck/tests/testthat/Bos_taurus_Bgee_14_2"

Building URLs to retrieve mapping of gene to organs from Bgee...
   URL successfully built (https://r.bgee.org/bgee14_2/?page=r_package&action=get_expression_calls&display_type=tsv&species_list=9913&attr_list=GENE_ID&attr_list=ANAT_ENTITY_ID&api_key=b7b4efc57a03bfa7d886b89ba582d181707f17f0c2ed3af43b29abd94bedbb15fb03720f65700e1ad3de35052bdebe3e7fe2f2c095d295c16e29eb9333832e7f&source=BgeeDB_R_package&source_version=2.21.3&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 "D:/biocbuild/bbs-3.15-bioc/meat/BgeeDB.Rcheck/tests/testthat/Bos_taurus_Bgee_14_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 14_2 was found in the download directory D:/biocbuild/bbs-3.15-bioc/meat/BgeeDB.Rcheck/tests/testthat. Data will not be redownloaded.

API key built: b7b4efc57a03bfa7d886b89ba582d181707f17f0c2ed3af43b29abd94bedbb15fb03720f65700e1ad3de35052bdebe3e7fe2f2c095d295c16e29eb9333832e7f

Saved annotation files in D:/biocbuild/bbs-3.15-bioc/meat/BgeeDB.Rcheck/tests/testthat/Drosophila_simulans_Bgee_14_2 folder.

Querying Bgee to get release information...

NOTE: the file describing Bgee species information for release 14_2 was found in the download directory D:/biocbuild/bbs-3.15-bioc/meat/BgeeDB.Rcheck/tests/testthat. Data will not be redownloaded.

API key built: b7b4efc57a03bfa7d886b89ba582d181707f17f0c2ed3af43b29abd94bedbb15fb03720f65700e1ad3de35052bdebe3e7fe2f2c095d295c16e29eb9333832e7f

NOTE: annotation files for this species were found in the download directory D:/biocbuild/bbs-3.15-bioc/meat/BgeeDB.Rcheck/tests/testthat/Mus_musculus_Bgee_14_2. Data will not be redownloaded.

Querying Bgee to get release information...

NOTE: the file describing Bgee species information for release 14_2 was found in the download directory D:/biocbuild/bbs-3.15-bioc/meat/BgeeDB.Rcheck/tests/testthat. Data will not be redownloaded.

API key built: b7b4efc57a03bfa7d886b89ba582d181707f17f0c2ed3af43b29abd94bedbb15fb03720f65700e1ad3de35052bdebe3e7fe2f2c095d295c16e29eb9333832e7f

NOTE: an organ relationships file was found in the download directory D:/biocbuild/bbs-3.15-bioc/meat/BgeeDB.Rcheck/tests/testthat/Bos_taurus_Bgee_14_2. Data will not be redownloaded.

NOTE: an organ names file was found in the download directory D:/biocbuild/bbs-3.15-bioc/meat/BgeeDB.Rcheck/tests/testthat/Bos_taurus_Bgee_14_2. Data will not be redownloaded.

NOTE: a gene to organs mapping file was found in the download directory D:/biocbuild/bbs-3.15-bioc/meat/BgeeDB.Rcheck/tests/testthat/Bos_taurus_Bgee_14_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......................

Building most specific Ontology terms...  (  61  Ontology terms found. )

Building DAG topology...................  (  379  Ontology terms and  619  relations. )

Annotating nodes (Can be long)..........  (  97  genes annotated to the Ontology terms. )
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 32 ]

[ FAIL 0 | WARN 1 | SKIP 0 | PASS 32 ]
> 
> proc.time()
   user  system elapsed 
  25.90    3.42  105.18