|
BgeeDB.Rcheck/tests_i386/testthat.Rout
R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
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 object is masked from 'package:base':
expand.grid
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=2.16.0)
Query to Bgee webservice successful!
API key built: e7b27c3ed08284be425042e791fd9e4525dc99e83a8186403f0f615f1e65f9e4d314a8db8de4d8675f897faa5a300655255251a56553d3e42f498094bd1d19c8
Saved annotation files in C:/Users/biocbuild/bbs-3.12-bioc/meat/BgeeDB.Rcheck/tests_i386/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=2.16.0)
Query to Bgee webservice successful!
API key built: e7b27c3ed08284be425042e791fd9e4525dc99e83a8186403f0f615f1e65f9e4d314a8db8de4d8675f897faa5a300655255251a56553d3e42f498094bd1d19c8
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 C:/Users/biocbuild/bbs-3.12-bioc/meat/BgeeDB.Rcheck/tests_i386/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 C:/Users/biocbuild/bbs-3.12-bioc/meat/BgeeDB.Rcheck/tests_i386/testthat. Data will not be redownloaded.
API key built: e7b27c3ed08284be425042e791fd9e4525dc99e83a8186403f0f615f1e65f9e4d314a8db8de4d8675f897faa5a300655255251a56553d3e42f498094bd1d19c8
NOTE: annotation files for this species were found in the download directory C:/Users/biocbuild/bbs-3.12-bioc/meat/BgeeDB.Rcheck/tests_i386/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 C:/Users/biocbuild/bbs-3.12-bioc/meat/BgeeDB.Rcheck/tests_i386/testthat. Data will not be redownloaded.
API key built: e7b27c3ed08284be425042e791fd9e4525dc99e83a8186403f0f615f1e65f9e4d314a8db8de4d8675f897faa5a300655255251a56553d3e42f498094bd1d19c8
Saved annotation files in C:/Users/biocbuild/bbs-3.12-bioc/meat/BgeeDB.Rcheck/tests_i386/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 C:/Users/biocbuild/bbs-3.12-bioc/meat/BgeeDB.Rcheck/tests_i386/testthat. Data will not be redownloaded.
API key built: e7b27c3ed08284be425042e791fd9e4525dc99e83a8186403f0f615f1e65f9e4d314a8db8de4d8675f897faa5a300655255251a56553d3e42f498094bd1d19c8
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 C:/Users/biocbuild/bbs-3.12-bioc/meat/BgeeDB.Rcheck/tests_i386/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 C:/Users/biocbuild/bbs-3.12-bioc/meat/BgeeDB.Rcheck/tests_i386/testthat. Data will not be redownloaded.
API key built: e7b27c3ed08284be425042e791fd9e4525dc99e83a8186403f0f615f1e65f9e4d314a8db8de4d8675f897faa5a300655255251a56553d3e42f498094bd1d19c8
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 C:/Users/biocbuild/bbs-3.12-bioc/meat/BgeeDB.Rcheck/tests_i386/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=2.16.0)
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=2.16.0)
Query to Bgee webservice successful!
API key built: e7b27c3ed08284be425042e791fd9e4525dc99e83a8186403f0f615f1e65f9e4d314a8db8de4d8675f897faa5a300655255251a56553d3e42f498094bd1d19c8
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=e7b27c3ed08284be425042e791fd9e4525dc99e83a8186403f0f615f1e65f9e4d314a8db8de4d8675f897faa5a300655255251a56553d3e42f498094bd1d19c8&source=BgeeDB_R_package&source_version=2.16.0)
Submitting URL to Bgee webservice (can be long)
Got results from Bgee webservice. Files are written in "C:/Users/biocbuild/bbs-3.12-bioc/meat/BgeeDB.Rcheck/tests_i386/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=e7b27c3ed08284be425042e791fd9e4525dc99e83a8186403f0f615f1e65f9e4d314a8db8de4d8675f897faa5a300655255251a56553d3e42f498094bd1d19c8&source=BgeeDB_R_package&source_version=2.16.0)
Submitting URL to Bgee webservice (can be long)
Got results from Bgee webservice. Files are written in "C:/Users/biocbuild/bbs-3.12-bioc/meat/BgeeDB.Rcheck/tests_i386/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=e7b27c3ed08284be425042e791fd9e4525dc99e83a8186403f0f615f1e65f9e4d314a8db8de4d8675f897faa5a300655255251a56553d3e42f498094bd1d19c8&source=BgeeDB_R_package&source_version=2.16.0&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 "C:/Users/biocbuild/bbs-3.12-bioc/meat/BgeeDB.Rcheck/tests_i386/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 C:/Users/biocbuild/bbs-3.12-bioc/meat/BgeeDB.Rcheck/tests_i386/testthat. Data will not be redownloaded.
API key built: e7b27c3ed08284be425042e791fd9e4525dc99e83a8186403f0f615f1e65f9e4d314a8db8de4d8675f897faa5a300655255251a56553d3e42f498094bd1d19c8
Saved annotation files in C:/Users/biocbuild/bbs-3.12-bioc/meat/BgeeDB.Rcheck/tests_i386/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 C:/Users/biocbuild/bbs-3.12-bioc/meat/BgeeDB.Rcheck/tests_i386/testthat. Data will not be redownloaded.
API key built: e7b27c3ed08284be425042e791fd9e4525dc99e83a8186403f0f615f1e65f9e4d314a8db8de4d8675f897faa5a300655255251a56553d3e42f498094bd1d19c8
NOTE: annotation files for this species were found in the download directory C:/Users/biocbuild/bbs-3.12-bioc/meat/BgeeDB.Rcheck/tests_i386/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 C:/Users/biocbuild/bbs-3.12-bioc/meat/BgeeDB.Rcheck/tests_i386/testthat. Data will not be redownloaded.
API key built: e7b27c3ed08284be425042e791fd9e4525dc99e83a8186403f0f615f1e65f9e4d314a8db8de4d8675f897faa5a300655255251a56553d3e42f498094bd1d19c8
NOTE: an organ relationships file was found in the download directory C:/Users/biocbuild/bbs-3.12-bioc/meat/BgeeDB.Rcheck/tests_i386/testthat/Bos_taurus_Bgee_14_2. Data will not be redownloaded.
NOTE: an organ names file was found in the download directory C:/Users/biocbuild/bbs-3.12-bioc/meat/BgeeDB.Rcheck/tests_i386/testthat/Bos_taurus_Bgee_14_2. Data will not be redownloaded.
NOTE: a gene to organs mapping file was found in the download directory C:/Users/biocbuild/bbs-3.12-bioc/meat/BgeeDB.Rcheck/tests_i386/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 0 | SKIP 0 | PASS 32 ]
>
> proc.time()
user system elapsed
30.23 2.54 112.36
|
BgeeDB.Rcheck/tests_x64/testthat.Rout
R version 4.0.5 (2021-03-31) -- "Shake and Throw"
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
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
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 object is masked from 'package:base':
expand.grid
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=2.16.0)
Query to Bgee webservice successful!
API key built: fd2b6a1a81e3d17f66210dc7c54528b94c2d51f684ee7e3ecf75d6a8fc85bad9e96893953aa589863980e60b6cb61561b9ffe1b78451f8d669dda14849e5bb48
Saved annotation files in C:/Users/biocbuild/bbs-3.12-bioc/meat/BgeeDB.Rcheck/tests_x64/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=2.16.0)
Query to Bgee webservice successful!
API key built: fd2b6a1a81e3d17f66210dc7c54528b94c2d51f684ee7e3ecf75d6a8fc85bad9e96893953aa589863980e60b6cb61561b9ffe1b78451f8d669dda14849e5bb48
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 C:/Users/biocbuild/bbs-3.12-bioc/meat/BgeeDB.Rcheck/tests_x64/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 C:/Users/biocbuild/bbs-3.12-bioc/meat/BgeeDB.Rcheck/tests_x64/testthat. Data will not be redownloaded.
API key built: fd2b6a1a81e3d17f66210dc7c54528b94c2d51f684ee7e3ecf75d6a8fc85bad9e96893953aa589863980e60b6cb61561b9ffe1b78451f8d669dda14849e5bb48
NOTE: annotation files for this species were found in the download directory C:/Users/biocbuild/bbs-3.12-bioc/meat/BgeeDB.Rcheck/tests_x64/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 C:/Users/biocbuild/bbs-3.12-bioc/meat/BgeeDB.Rcheck/tests_x64/testthat. Data will not be redownloaded.
API key built: fd2b6a1a81e3d17f66210dc7c54528b94c2d51f684ee7e3ecf75d6a8fc85bad9e96893953aa589863980e60b6cb61561b9ffe1b78451f8d669dda14849e5bb48
Saved annotation files in C:/Users/biocbuild/bbs-3.12-bioc/meat/BgeeDB.Rcheck/tests_x64/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 C:/Users/biocbuild/bbs-3.12-bioc/meat/BgeeDB.Rcheck/tests_x64/testthat. Data will not be redownloaded.
API key built: fd2b6a1a81e3d17f66210dc7c54528b94c2d51f684ee7e3ecf75d6a8fc85bad9e96893953aa589863980e60b6cb61561b9ffe1b78451f8d669dda14849e5bb48
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 C:/Users/biocbuild/bbs-3.12-bioc/meat/BgeeDB.Rcheck/tests_x64/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 C:/Users/biocbuild/bbs-3.12-bioc/meat/BgeeDB.Rcheck/tests_x64/testthat. Data will not be redownloaded.
API key built: fd2b6a1a81e3d17f66210dc7c54528b94c2d51f684ee7e3ecf75d6a8fc85bad9e96893953aa589863980e60b6cb61561b9ffe1b78451f8d669dda14849e5bb48
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 C:/Users/biocbuild/bbs-3.12-bioc/meat/BgeeDB.Rcheck/tests_x64/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=2.16.0)
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=2.16.0)
Query to Bgee webservice successful!
API key built: fd2b6a1a81e3d17f66210dc7c54528b94c2d51f684ee7e3ecf75d6a8fc85bad9e96893953aa589863980e60b6cb61561b9ffe1b78451f8d669dda14849e5bb48
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=fd2b6a1a81e3d17f66210dc7c54528b94c2d51f684ee7e3ecf75d6a8fc85bad9e96893953aa589863980e60b6cb61561b9ffe1b78451f8d669dda14849e5bb48&source=BgeeDB_R_package&source_version=2.16.0)
Submitting URL to Bgee webservice (can be long)
Got results from Bgee webservice. Files are written in "C:/Users/biocbuild/bbs-3.12-bioc/meat/BgeeDB.Rcheck/tests_x64/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=fd2b6a1a81e3d17f66210dc7c54528b94c2d51f684ee7e3ecf75d6a8fc85bad9e96893953aa589863980e60b6cb61561b9ffe1b78451f8d669dda14849e5bb48&source=BgeeDB_R_package&source_version=2.16.0)
Submitting URL to Bgee webservice (can be long)
Got results from Bgee webservice. Files are written in "C:/Users/biocbuild/bbs-3.12-bioc/meat/BgeeDB.Rcheck/tests_x64/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=fd2b6a1a81e3d17f66210dc7c54528b94c2d51f684ee7e3ecf75d6a8fc85bad9e96893953aa589863980e60b6cb61561b9ffe1b78451f8d669dda14849e5bb48&source=BgeeDB_R_package&source_version=2.16.0&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 "C:/Users/biocbuild/bbs-3.12-bioc/meat/BgeeDB.Rcheck/tests_x64/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 C:/Users/biocbuild/bbs-3.12-bioc/meat/BgeeDB.Rcheck/tests_x64/testthat. Data will not be redownloaded.
API key built: fd2b6a1a81e3d17f66210dc7c54528b94c2d51f684ee7e3ecf75d6a8fc85bad9e96893953aa589863980e60b6cb61561b9ffe1b78451f8d669dda14849e5bb48
Saved annotation files in C:/Users/biocbuild/bbs-3.12-bioc/meat/BgeeDB.Rcheck/tests_x64/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 C:/Users/biocbuild/bbs-3.12-bioc/meat/BgeeDB.Rcheck/tests_x64/testthat. Data will not be redownloaded.
API key built: fd2b6a1a81e3d17f66210dc7c54528b94c2d51f684ee7e3ecf75d6a8fc85bad9e96893953aa589863980e60b6cb61561b9ffe1b78451f8d669dda14849e5bb48
NOTE: annotation files for this species were found in the download directory C:/Users/biocbuild/bbs-3.12-bioc/meat/BgeeDB.Rcheck/tests_x64/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 C:/Users/biocbuild/bbs-3.12-bioc/meat/BgeeDB.Rcheck/tests_x64/testthat. Data will not be redownloaded.
API key built: fd2b6a1a81e3d17f66210dc7c54528b94c2d51f684ee7e3ecf75d6a8fc85bad9e96893953aa589863980e60b6cb61561b9ffe1b78451f8d669dda14849e5bb48
NOTE: an organ relationships file was found in the download directory C:/Users/biocbuild/bbs-3.12-bioc/meat/BgeeDB.Rcheck/tests_x64/testthat/Bos_taurus_Bgee_14_2. Data will not be redownloaded.
NOTE: an organ names file was found in the download directory C:/Users/biocbuild/bbs-3.12-bioc/meat/BgeeDB.Rcheck/tests_x64/testthat/Bos_taurus_Bgee_14_2. Data will not be redownloaded.
NOTE: a gene to organs mapping file was found in the download directory C:/Users/biocbuild/bbs-3.12-bioc/meat/BgeeDB.Rcheck/tests_x64/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 0 | SKIP 0 | PASS 32 ]
>
> proc.time()
user system elapsed
28.87 2.31 126.51
|
