|
BgeeDB.Rcheck/tests_i386/testthat.Rout
R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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, 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_1...
Submitting URL to Bgee webservice... (https://r.bgee.org/bgee14_1/?page=r_package&action=get_all_species&display_type=tsv&source=BgeeDB_R_package&source_version=2.14.5)
Query to Bgee webservice successful!
API key built: 5b83848ef7fb875c4815428ad1dd0d1c7cb65ee24316beea7a81c7add8e9a125af326e44a622aa5f80840f7ff5605d3c4ff2049e03430382fc5faf4c36efd585
Saved annotation files in C:/Users/biocbuild/bbs-3.11-bioc/meat/BgeeDB.Rcheck/tests_i386/testthat/Mus_musculus_Bgee_14_1 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=2.14.5)
Query to Bgee webservice successful!
API key built: 5b83848ef7fb875c4815428ad1dd0d1c7cb65ee24316beea7a81c7add8e9a125af326e44a622aa5f80840f7ff5605d3c4ff2049e03430382fc5faf4c36efd585
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-3.11-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_1 was found in the download directory C:/Users/biocbuild/bbs-3.11-bioc/meat/BgeeDB.Rcheck/tests_i386/testthat. Data will not be redownloaded.
API key built: 5b83848ef7fb875c4815428ad1dd0d1c7cb65ee24316beea7a81c7add8e9a125af326e44a622aa5f80840f7ff5605d3c4ff2049e03430382fc5faf4c36efd585
NOTE: annotation files for this species were found in the download directory C:/Users/biocbuild/bbs-3.11-bioc/meat/BgeeDB.Rcheck/tests_i386/testthat/Mus_musculus_Bgee_14_1. Data will not be redownloaded.
Querying Bgee to get release information...
NOTE: the file describing Bgee species information for release 14_1 was found in the download directory C:/Users/biocbuild/bbs-3.11-bioc/meat/BgeeDB.Rcheck/tests_i386/testthat. Data will not be redownloaded.
API key built: 5b83848ef7fb875c4815428ad1dd0d1c7cb65ee24316beea7a81c7add8e9a125af326e44a622aa5f80840f7ff5605d3c4ff2049e03430382fc5faf4c36efd585
Saved annotation files in C:/Users/biocbuild/bbs-3.11-bioc/meat/BgeeDB.Rcheck/tests_i386/testthat/Mus_musculus_Bgee_14_1 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-3.11-bioc/meat/BgeeDB.Rcheck/tests_i386/testthat. Data will not be redownloaded.
API key built: 5b83848ef7fb875c4815428ad1dd0d1c7cb65ee24316beea7a81c7add8e9a125af326e44a622aa5f80840f7ff5605d3c4ff2049e03430382fc5faf4c36efd585
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-3.11-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-3.11-bioc/meat/BgeeDB.Rcheck/tests_i386/testthat. Data will not be redownloaded.
API key built: 5b83848ef7fb875c4815428ad1dd0d1c7cb65ee24316beea7a81c7add8e9a125af326e44a622aa5f80840f7ff5605d3c4ff2049e03430382fc5faf4c36efd585
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-3.11-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_1...
Submitting URL to Bgee webservice... (https://r.bgee.org/bgee14_1/?page=r_package&action=get_all_species&display_type=tsv&source=BgeeDB_R_package&source_version=2.14.5)
Query to Bgee webservice successful!
Querying Bgee to get release information...
Building URL to query species in Bgee release 14_1...
Submitting URL to Bgee webservice... (https://r.bgee.org/bgee14_1/?page=r_package&action=get_all_species&display_type=tsv&source=BgeeDB_R_package&source_version=2.14.5)
Query to Bgee webservice successful!
API key built: 5b83848ef7fb875c4815428ad1dd0d1c7cb65ee24316beea7a81c7add8e9a125af326e44a622aa5f80840f7ff5605d3c4ff2049e03430382fc5faf4c36efd585
Building URLs to retrieve organ relationships from Bgee.........
URL successfully built (https://r.bgee.org/bgee14_1/?page=r_package&action=get_anat_entity_relations&display_type=tsv&species_list=9913&attr_list=SOURCE_ID&attr_list=TARGET_ID&api_key=5b83848ef7fb875c4815428ad1dd0d1c7cb65ee24316beea7a81c7add8e9a125af326e44a622aa5f80840f7ff5605d3c4ff2049e03430382fc5faf4c36efd585&source=BgeeDB_R_package&source_version=2.14.5)
Submitting URL to Bgee webservice (can be long)
Got results from Bgee webservice. Files are written in "C:/Users/biocbuild/bbs-3.11-bioc/meat/BgeeDB.Rcheck/tests_i386/testthat/Bos_taurus_Bgee_14_1"
Building URLs to retrieve organ names from Bgee.................
URL successfully built (https://r.bgee.org/bgee14_1/?page=r_package&action=get_anat_entities&display_type=tsv&species_list=9913&attr_list=ID&attr_list=NAME&api_key=5b83848ef7fb875c4815428ad1dd0d1c7cb65ee24316beea7a81c7add8e9a125af326e44a622aa5f80840f7ff5605d3c4ff2049e03430382fc5faf4c36efd585&source=BgeeDB_R_package&source_version=2.14.5)
Submitting URL to Bgee webservice (can be long)
Got results from Bgee webservice. Files are written in "C:/Users/biocbuild/bbs-3.11-bioc/meat/BgeeDB.Rcheck/tests_i386/testthat/Bos_taurus_Bgee_14_1"
Building URLs to retrieve mapping of gene to organs from Bgee...
URL successfully built (https://r.bgee.org/bgee14_1/?page=r_package&action=get_expression_calls&display_type=tsv&species_list=9913&attr_list=GENE_ID&attr_list=ANAT_ENTITY_ID&api_key=5b83848ef7fb875c4815428ad1dd0d1c7cb65ee24316beea7a81c7add8e9a125af326e44a622aa5f80840f7ff5605d3c4ff2049e03430382fc5faf4c36efd585&source=BgeeDB_R_package&source_version=2.14.5&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-3.11-bioc/meat/BgeeDB.Rcheck/tests_i386/testthat/Bos_taurus_Bgee_14_1"
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_1 was found in the download directory C:/Users/biocbuild/bbs-3.11-bioc/meat/BgeeDB.Rcheck/tests_i386/testthat. Data will not be redownloaded.
API key built: 5b83848ef7fb875c4815428ad1dd0d1c7cb65ee24316beea7a81c7add8e9a125af326e44a622aa5f80840f7ff5605d3c4ff2049e03430382fc5faf4c36efd585
Saved annotation files in C:/Users/biocbuild/bbs-3.11-bioc/meat/BgeeDB.Rcheck/tests_i386/testthat/Drosophila_simulans_Bgee_14_1 folder.
Querying Bgee to get release information...
NOTE: the file describing Bgee species information for release 14_1 was found in the download directory C:/Users/biocbuild/bbs-3.11-bioc/meat/BgeeDB.Rcheck/tests_i386/testthat. Data will not be redownloaded.
API key built: 5b83848ef7fb875c4815428ad1dd0d1c7cb65ee24316beea7a81c7add8e9a125af326e44a622aa5f80840f7ff5605d3c4ff2049e03430382fc5faf4c36efd585
NOTE: annotation files for this species were found in the download directory C:/Users/biocbuild/bbs-3.11-bioc/meat/BgeeDB.Rcheck/tests_i386/testthat/Mus_musculus_Bgee_14_1. Data will not be redownloaded.
Querying Bgee to get release information...
NOTE: the file describing Bgee species information for release 14_1 was found in the download directory C:/Users/biocbuild/bbs-3.11-bioc/meat/BgeeDB.Rcheck/tests_i386/testthat. Data will not be redownloaded.
API key built: 5b83848ef7fb875c4815428ad1dd0d1c7cb65ee24316beea7a81c7add8e9a125af326e44a622aa5f80840f7ff5605d3c4ff2049e03430382fc5faf4c36efd585
NOTE: an organ relationships file was found in the download directory C:/Users/biocbuild/bbs-3.11-bioc/meat/BgeeDB.Rcheck/tests_i386/testthat/Bos_taurus_Bgee_14_1. Data will not be redownloaded.
NOTE: an organ names file was found in the download directory C:/Users/biocbuild/bbs-3.11-bioc/meat/BgeeDB.Rcheck/tests_i386/testthat/Bos_taurus_Bgee_14_1. Data will not be redownloaded.
NOTE: a gene to organs mapping file was found in the download directory C:/Users/biocbuild/bbs-3.11-bioc/meat/BgeeDB.Rcheck/tests_i386/testthat/Bos_taurus_Bgee_14_1. 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... ( 14 Ontology terms found. )
Building DAG topology................... ( 145 Ontology terms and 211 relations. )
Annotating nodes (Can be long).......... ( 97 genes annotated to the Ontology terms. )
== testthat results ===========================================================
[ OK: 32 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
24.92 1.70 85.00
|
BgeeDB.Rcheck/tests_x64/testthat.Rout
R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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, 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_1...
Submitting URL to Bgee webservice... (https://r.bgee.org/bgee14_1/?page=r_package&action=get_all_species&display_type=tsv&source=BgeeDB_R_package&source_version=2.14.5)
Query to Bgee webservice successful!
API key built: 70e62e284bfee2ea84ac6030ca50c1c183e850d5343075d2d5e30c715d08ec0ded968ae445b78284861a6b97531d717324c5afbd8f6de8222730d591a0d135b3
Saved annotation files in C:/Users/biocbuild/bbs-3.11-bioc/meat/BgeeDB.Rcheck/tests_x64/testthat/Mus_musculus_Bgee_14_1 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=2.14.5)
Query to Bgee webservice successful!
API key built: 70e62e284bfee2ea84ac6030ca50c1c183e850d5343075d2d5e30c715d08ec0ded968ae445b78284861a6b97531d717324c5afbd8f6de8222730d591a0d135b3
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-3.11-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_1 was found in the download directory C:/Users/biocbuild/bbs-3.11-bioc/meat/BgeeDB.Rcheck/tests_x64/testthat. Data will not be redownloaded.
API key built: 70e62e284bfee2ea84ac6030ca50c1c183e850d5343075d2d5e30c715d08ec0ded968ae445b78284861a6b97531d717324c5afbd8f6de8222730d591a0d135b3
NOTE: annotation files for this species were found in the download directory C:/Users/biocbuild/bbs-3.11-bioc/meat/BgeeDB.Rcheck/tests_x64/testthat/Mus_musculus_Bgee_14_1. Data will not be redownloaded.
Querying Bgee to get release information...
NOTE: the file describing Bgee species information for release 14_1 was found in the download directory C:/Users/biocbuild/bbs-3.11-bioc/meat/BgeeDB.Rcheck/tests_x64/testthat. Data will not be redownloaded.
API key built: 70e62e284bfee2ea84ac6030ca50c1c183e850d5343075d2d5e30c715d08ec0ded968ae445b78284861a6b97531d717324c5afbd8f6de8222730d591a0d135b3
Saved annotation files in C:/Users/biocbuild/bbs-3.11-bioc/meat/BgeeDB.Rcheck/tests_x64/testthat/Mus_musculus_Bgee_14_1 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-3.11-bioc/meat/BgeeDB.Rcheck/tests_x64/testthat. Data will not be redownloaded.
API key built: 70e62e284bfee2ea84ac6030ca50c1c183e850d5343075d2d5e30c715d08ec0ded968ae445b78284861a6b97531d717324c5afbd8f6de8222730d591a0d135b3
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-3.11-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-3.11-bioc/meat/BgeeDB.Rcheck/tests_x64/testthat. Data will not be redownloaded.
API key built: 70e62e284bfee2ea84ac6030ca50c1c183e850d5343075d2d5e30c715d08ec0ded968ae445b78284861a6b97531d717324c5afbd8f6de8222730d591a0d135b3
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-3.11-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_1...
Submitting URL to Bgee webservice... (https://r.bgee.org/bgee14_1/?page=r_package&action=get_all_species&display_type=tsv&source=BgeeDB_R_package&source_version=2.14.5)
Query to Bgee webservice successful!
Querying Bgee to get release information...
Building URL to query species in Bgee release 14_1...
Submitting URL to Bgee webservice... (https://r.bgee.org/bgee14_1/?page=r_package&action=get_all_species&display_type=tsv&source=BgeeDB_R_package&source_version=2.14.5)
Query to Bgee webservice successful!
API key built: 70e62e284bfee2ea84ac6030ca50c1c183e850d5343075d2d5e30c715d08ec0ded968ae445b78284861a6b97531d717324c5afbd8f6de8222730d591a0d135b3
Building URLs to retrieve organ relationships from Bgee.........
URL successfully built (https://r.bgee.org/bgee14_1/?page=r_package&action=get_anat_entity_relations&display_type=tsv&species_list=9913&attr_list=SOURCE_ID&attr_list=TARGET_ID&api_key=70e62e284bfee2ea84ac6030ca50c1c183e850d5343075d2d5e30c715d08ec0ded968ae445b78284861a6b97531d717324c5afbd8f6de8222730d591a0d135b3&source=BgeeDB_R_package&source_version=2.14.5)
Submitting URL to Bgee webservice (can be long)
Got results from Bgee webservice. Files are written in "C:/Users/biocbuild/bbs-3.11-bioc/meat/BgeeDB.Rcheck/tests_x64/testthat/Bos_taurus_Bgee_14_1"
Building URLs to retrieve organ names from Bgee.................
URL successfully built (https://r.bgee.org/bgee14_1/?page=r_package&action=get_anat_entities&display_type=tsv&species_list=9913&attr_list=ID&attr_list=NAME&api_key=70e62e284bfee2ea84ac6030ca50c1c183e850d5343075d2d5e30c715d08ec0ded968ae445b78284861a6b97531d717324c5afbd8f6de8222730d591a0d135b3&source=BgeeDB_R_package&source_version=2.14.5)
Submitting URL to Bgee webservice (can be long)
Got results from Bgee webservice. Files are written in "C:/Users/biocbuild/bbs-3.11-bioc/meat/BgeeDB.Rcheck/tests_x64/testthat/Bos_taurus_Bgee_14_1"
Building URLs to retrieve mapping of gene to organs from Bgee...
URL successfully built (https://r.bgee.org/bgee14_1/?page=r_package&action=get_expression_calls&display_type=tsv&species_list=9913&attr_list=GENE_ID&attr_list=ANAT_ENTITY_ID&api_key=70e62e284bfee2ea84ac6030ca50c1c183e850d5343075d2d5e30c715d08ec0ded968ae445b78284861a6b97531d717324c5afbd8f6de8222730d591a0d135b3&source=BgeeDB_R_package&source_version=2.14.5&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-3.11-bioc/meat/BgeeDB.Rcheck/tests_x64/testthat/Bos_taurus_Bgee_14_1"
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_1 was found in the download directory C:/Users/biocbuild/bbs-3.11-bioc/meat/BgeeDB.Rcheck/tests_x64/testthat. Data will not be redownloaded.
API key built: 70e62e284bfee2ea84ac6030ca50c1c183e850d5343075d2d5e30c715d08ec0ded968ae445b78284861a6b97531d717324c5afbd8f6de8222730d591a0d135b3
Saved annotation files in C:/Users/biocbuild/bbs-3.11-bioc/meat/BgeeDB.Rcheck/tests_x64/testthat/Drosophila_simulans_Bgee_14_1 folder.
Querying Bgee to get release information...
NOTE: the file describing Bgee species information for release 14_1 was found in the download directory C:/Users/biocbuild/bbs-3.11-bioc/meat/BgeeDB.Rcheck/tests_x64/testthat. Data will not be redownloaded.
API key built: 70e62e284bfee2ea84ac6030ca50c1c183e850d5343075d2d5e30c715d08ec0ded968ae445b78284861a6b97531d717324c5afbd8f6de8222730d591a0d135b3
NOTE: annotation files for this species were found in the download directory C:/Users/biocbuild/bbs-3.11-bioc/meat/BgeeDB.Rcheck/tests_x64/testthat/Mus_musculus_Bgee_14_1. Data will not be redownloaded.
Querying Bgee to get release information...
NOTE: the file describing Bgee species information for release 14_1 was found in the download directory C:/Users/biocbuild/bbs-3.11-bioc/meat/BgeeDB.Rcheck/tests_x64/testthat. Data will not be redownloaded.
API key built: 70e62e284bfee2ea84ac6030ca50c1c183e850d5343075d2d5e30c715d08ec0ded968ae445b78284861a6b97531d717324c5afbd8f6de8222730d591a0d135b3
NOTE: an organ relationships file was found in the download directory C:/Users/biocbuild/bbs-3.11-bioc/meat/BgeeDB.Rcheck/tests_x64/testthat/Bos_taurus_Bgee_14_1. Data will not be redownloaded.
NOTE: an organ names file was found in the download directory C:/Users/biocbuild/bbs-3.11-bioc/meat/BgeeDB.Rcheck/tests_x64/testthat/Bos_taurus_Bgee_14_1. Data will not be redownloaded.
NOTE: a gene to organs mapping file was found in the download directory C:/Users/biocbuild/bbs-3.11-bioc/meat/BgeeDB.Rcheck/tests_x64/testthat/Bos_taurus_Bgee_14_1. 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... ( 14 Ontology terms found. )
Building DAG topology................... ( 145 Ontology terms and 211 relations. )
Annotating nodes (Can be long).......... ( 97 genes annotated to the Ontology terms. )
== testthat results ===========================================================
[ OK: 32 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
22.92 1.34 81.84
|
