Julien Wollbrett
| Snapshot Date: 2022-04-10 01:55:06 -0400 (Sun, 10 Apr 2022) |
| git_url: https://git.bioconductor.org/packages/BgeeDB |
| git_branch: RELEASE_3_14 |
| git_last_commit: e7dc7fe |
| git_last_commit_date: 2022-03-28 12:38:43 -0400 (Mon, 28 Mar 2022) |
| Back to Multiple platform build/check report for BioC 3.14 |
|
This page was generated on 2022-04-11 12:05:55 -0400 (Mon, 11 Apr 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4323 |
| tokay2 | Windows Server 2012 R2 Standard | x64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4077 |
| machv2 | macOS 10.14.6 Mojave | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4136 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
|
To the developers/maintainers of the BgeeDB package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BgeeDB.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 141/2083 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BgeeDB 2.20.1 (landing page) Julien Wollbrett
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: BgeeDB |
| Version: 2.20.1 |
| Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BgeeDB.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings BgeeDB_2.20.1.tar.gz |
| StartedAt: 2022-04-10 16:13:06 -0400 (Sun, 10 Apr 2022) |
| EndedAt: 2022-04-10 16:28:24 -0400 (Sun, 10 Apr 2022) |
| EllapsedTime: 918.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BgeeDB.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BgeeDB.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings BgeeDB_2.20.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/BgeeDB.Rcheck'
* using R version 4.1.3 (2022-03-10)
* 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 '2.20.1'
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
geneList 12.57 1.03 43.14
makeTable 12.25 0.92 60.39
topAnat 8.25 0.75 9.77
loadTopAnatData 8.25 0.48 98.34
formatData 6.29 0.70 17.93
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
geneList 12.08 0.52 39.07
makeTable 10.76 0.71 47.86
loadTopAnatData 8.75 0.42 79.73
topAnat 6.05 0.56 7.36
formatData 5.39 0.62 14.44
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'testthat.R'
OK
** running tests for arch 'x64' ...
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: OK
BgeeDB.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/BgeeDB_2.20.1.tar.gz && rm -rf BgeeDB.buildbin-libdir && mkdir BgeeDB.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=BgeeDB.buildbin-libdir BgeeDB_2.20.1.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL BgeeDB_2.20.1.zip && rm BgeeDB_2.20.1.tar.gz BgeeDB_2.20.1.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 72281 100 72281 0 0 453k 0 --:--:-- --:--:-- --:--:-- 458k
install for i386
* 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
install for x64
* installing *source* package 'BgeeDB' ...
** testing if installed package can be loaded
groupGOTerms: GOBPTerm, GOMFTerm, GOCCTerm environments built.
* MD5 sums
packaged installation of 'BgeeDB' as BgeeDB_2.20.1.zip
* DONE (BgeeDB)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'BgeeDB' successfully unpacked and MD5 sums checked
|
BgeeDB.Rcheck/tests_i386/testthat.Rout
R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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
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 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=2.20.1)
Query to Bgee webservice successful!
API key built: b6acc682b83b2ebea79c2d6c5e98e6e4fb7ed08a47118f4f480a8ff1c2df968af56cbc84d73f429201d8009cf069d2938795112085a8d858a6ea795ca27bc738
Saved annotation files in C:/Users/biocbuild/bbs-3.14-bioc/meat/BgeeDB.Rcheck/tests_i386/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=2.20.1)
Query to Bgee webservice successful!
API key built: b6acc682b83b2ebea79c2d6c5e98e6e4fb7ed08a47118f4f480a8ff1c2df968af56cbc84d73f429201d8009cf069d2938795112085a8d858a6ea795ca27bc738
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-3.14-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 15_0 was found in the download directory C:/Users/biocbuild/bbs-3.14-bioc/meat/BgeeDB.Rcheck/tests_i386/testthat. Data will not be redownloaded.
API key built: b6acc682b83b2ebea79c2d6c5e98e6e4fb7ed08a47118f4f480a8ff1c2df968af56cbc84d73f429201d8009cf069d2938795112085a8d858a6ea795ca27bc738
NOTE: annotation files for this species were found in the download directory C:/Users/biocbuild/bbs-3.14-bioc/meat/BgeeDB.Rcheck/tests_i386/testthat/Mus_musculus_Bgee_15_0. Data will not be redownloaded.
Querying Bgee to get release information...
NOTE: the file describing Bgee species information for release 15_0 was found in the download directory C:/Users/biocbuild/bbs-3.14-bioc/meat/BgeeDB.Rcheck/tests_i386/testthat. Data will not be redownloaded.
API key built: b6acc682b83b2ebea79c2d6c5e98e6e4fb7ed08a47118f4f480a8ff1c2df968af56cbc84d73f429201d8009cf069d2938795112085a8d858a6ea795ca27bc738
Saved annotation files in C:/Users/biocbuild/bbs-3.14-bioc/meat/BgeeDB.Rcheck/tests_i386/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 C:/Users/biocbuild/bbs-3.14-bioc/meat/BgeeDB.Rcheck/tests_i386/testthat. Data will not be redownloaded.
API key built: b6acc682b83b2ebea79c2d6c5e98e6e4fb7ed08a47118f4f480a8ff1c2df968af56cbc84d73f429201d8009cf069d2938795112085a8d858a6ea795ca27bc738
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-3.14-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-3.14-bioc/meat/BgeeDB.Rcheck/tests_i386/testthat. Data will not be redownloaded.
API key built: b6acc682b83b2ebea79c2d6c5e98e6e4fb7ed08a47118f4f480a8ff1c2df968af56cbc84d73f429201d8009cf069d2938795112085a8d858a6ea795ca27bc738
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-3.14-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=2.20.1)
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 C:/Users/biocbuild/bbs-3.14-bioc/meat/BgeeDB.Rcheck/tests_i386/testthat. Data will not be redownloaded.
API key built: b6acc682b83b2ebea79c2d6c5e98e6e4fb7ed08a47118f4f480a8ff1c2df968af56cbc84d73f429201d8009cf069d2938795112085a8d858a6ea795ca27bc738
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=b6acc682b83b2ebea79c2d6c5e98e6e4fb7ed08a47118f4f480a8ff1c2df968af56cbc84d73f429201d8009cf069d2938795112085a8d858a6ea795ca27bc738&source=BgeeDB_R_package&source_version=2.20.1)
Submitting URL to Bgee webservice (can be long)
Got results from Bgee webservice. Files are written in "C:/Users/biocbuild/bbs-3.14-bioc/meat/BgeeDB.Rcheck/tests_i386/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=b6acc682b83b2ebea79c2d6c5e98e6e4fb7ed08a47118f4f480a8ff1c2df968af56cbc84d73f429201d8009cf069d2938795112085a8d858a6ea795ca27bc738&source=BgeeDB_R_package&source_version=2.20.1)
Submitting URL to Bgee webservice (can be long)
Got results from Bgee webservice. Files are written in "C:/Users/biocbuild/bbs-3.14-bioc/meat/BgeeDB.Rcheck/tests_i386/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=b6acc682b83b2ebea79c2d6c5e98e6e4fb7ed08a47118f4f480a8ff1c2df968af56cbc84d73f429201d8009cf069d2938795112085a8d858a6ea795ca27bc738&source=BgeeDB_R_package&source_version=2.20.1&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-3.14-bioc/meat/BgeeDB.Rcheck/tests_i386/testthat/Bos_taurus_Bgee_15_0"
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_0 was found in the download directory C:/Users/biocbuild/bbs-3.14-bioc/meat/BgeeDB.Rcheck/tests_i386/testthat. Data will not be redownloaded.
API key built: b6acc682b83b2ebea79c2d6c5e98e6e4fb7ed08a47118f4f480a8ff1c2df968af56cbc84d73f429201d8009cf069d2938795112085a8d858a6ea795ca27bc738
Saved annotation files in C:/Users/biocbuild/bbs-3.14-bioc/meat/BgeeDB.Rcheck/tests_i386/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 C:/Users/biocbuild/bbs-3.14-bioc/meat/BgeeDB.Rcheck/tests_i386/testthat. Data will not be redownloaded.
API key built: b6acc682b83b2ebea79c2d6c5e98e6e4fb7ed08a47118f4f480a8ff1c2df968af56cbc84d73f429201d8009cf069d2938795112085a8d858a6ea795ca27bc738
NOTE: annotation files for this species were found in the download directory C:/Users/biocbuild/bbs-3.14-bioc/meat/BgeeDB.Rcheck/tests_i386/testthat/Mus_musculus_Bgee_15_0. Data will not be redownloaded.
Querying Bgee to get release information...
NOTE: the file describing Bgee species information for release 15_0 was found in the download directory C:/Users/biocbuild/bbs-3.14-bioc/meat/BgeeDB.Rcheck/tests_i386/testthat. Data will not be redownloaded.
API key built: b6acc682b83b2ebea79c2d6c5e98e6e4fb7ed08a47118f4f480a8ff1c2df968af56cbc84d73f429201d8009cf069d2938795112085a8d858a6ea795ca27bc738
NOTE: an organ relationships file was found in the download directory C:/Users/biocbuild/bbs-3.14-bioc/meat/BgeeDB.Rcheck/tests_i386/testthat/Bos_taurus_Bgee_15_0. Data will not be redownloaded.
NOTE: an organ names file was found in the download directory C:/Users/biocbuild/bbs-3.14-bioc/meat/BgeeDB.Rcheck/tests_i386/testthat/Bos_taurus_Bgee_15_0. Data will not be redownloaded.
NOTE: a gene to organs mapping file was found in the download directory C:/Users/biocbuild/bbs-3.14-bioc/meat/BgeeDB.Rcheck/tests_i386/testthat/Bos_taurus_Bgee_15_0. 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 1 | SKIP 0 | PASS 32 ]
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 32 ]
>
> proc.time()
user system elapsed
38.84 3.90 141.11
|
BgeeDB.Rcheck/tests_x64/testthat.Rout
R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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 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=2.20.1)
Query to Bgee webservice successful!
API key built: 7cb00f7734bc1341352a4181373b6d014a68f8e24c6893009a4ab69380c33b6f75c51647b6c4c725245acc6fa72ea5a9ace2aca6716b40621a41c039d28fe3d2
Saved annotation files in C:/Users/biocbuild/bbs-3.14-bioc/meat/BgeeDB.Rcheck/tests_x64/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=2.20.1)
Query to Bgee webservice successful!
API key built: 7cb00f7734bc1341352a4181373b6d014a68f8e24c6893009a4ab69380c33b6f75c51647b6c4c725245acc6fa72ea5a9ace2aca6716b40621a41c039d28fe3d2
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-3.14-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 15_0 was found in the download directory C:/Users/biocbuild/bbs-3.14-bioc/meat/BgeeDB.Rcheck/tests_x64/testthat. Data will not be redownloaded.
API key built: 7cb00f7734bc1341352a4181373b6d014a68f8e24c6893009a4ab69380c33b6f75c51647b6c4c725245acc6fa72ea5a9ace2aca6716b40621a41c039d28fe3d2
NOTE: annotation files for this species were found in the download directory C:/Users/biocbuild/bbs-3.14-bioc/meat/BgeeDB.Rcheck/tests_x64/testthat/Mus_musculus_Bgee_15_0. Data will not be redownloaded.
Querying Bgee to get release information...
NOTE: the file describing Bgee species information for release 15_0 was found in the download directory C:/Users/biocbuild/bbs-3.14-bioc/meat/BgeeDB.Rcheck/tests_x64/testthat. Data will not be redownloaded.
API key built: 7cb00f7734bc1341352a4181373b6d014a68f8e24c6893009a4ab69380c33b6f75c51647b6c4c725245acc6fa72ea5a9ace2aca6716b40621a41c039d28fe3d2
Saved annotation files in C:/Users/biocbuild/bbs-3.14-bioc/meat/BgeeDB.Rcheck/tests_x64/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 C:/Users/biocbuild/bbs-3.14-bioc/meat/BgeeDB.Rcheck/tests_x64/testthat. Data will not be redownloaded.
API key built: 7cb00f7734bc1341352a4181373b6d014a68f8e24c6893009a4ab69380c33b6f75c51647b6c4c725245acc6fa72ea5a9ace2aca6716b40621a41c039d28fe3d2
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-3.14-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-3.14-bioc/meat/BgeeDB.Rcheck/tests_x64/testthat. Data will not be redownloaded.
API key built: 7cb00f7734bc1341352a4181373b6d014a68f8e24c6893009a4ab69380c33b6f75c51647b6c4c725245acc6fa72ea5a9ace2aca6716b40621a41c039d28fe3d2
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-3.14-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=2.20.1)
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 C:/Users/biocbuild/bbs-3.14-bioc/meat/BgeeDB.Rcheck/tests_x64/testthat. Data will not be redownloaded.
API key built: 7cb00f7734bc1341352a4181373b6d014a68f8e24c6893009a4ab69380c33b6f75c51647b6c4c725245acc6fa72ea5a9ace2aca6716b40621a41c039d28fe3d2
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=7cb00f7734bc1341352a4181373b6d014a68f8e24c6893009a4ab69380c33b6f75c51647b6c4c725245acc6fa72ea5a9ace2aca6716b40621a41c039d28fe3d2&source=BgeeDB_R_package&source_version=2.20.1)
Submitting URL to Bgee webservice (can be long)
Got results from Bgee webservice. Files are written in "C:/Users/biocbuild/bbs-3.14-bioc/meat/BgeeDB.Rcheck/tests_x64/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=7cb00f7734bc1341352a4181373b6d014a68f8e24c6893009a4ab69380c33b6f75c51647b6c4c725245acc6fa72ea5a9ace2aca6716b40621a41c039d28fe3d2&source=BgeeDB_R_package&source_version=2.20.1)
Submitting URL to Bgee webservice (can be long)
Got results from Bgee webservice. Files are written in "C:/Users/biocbuild/bbs-3.14-bioc/meat/BgeeDB.Rcheck/tests_x64/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=7cb00f7734bc1341352a4181373b6d014a68f8e24c6893009a4ab69380c33b6f75c51647b6c4c725245acc6fa72ea5a9ace2aca6716b40621a41c039d28fe3d2&source=BgeeDB_R_package&source_version=2.20.1&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-3.14-bioc/meat/BgeeDB.Rcheck/tests_x64/testthat/Bos_taurus_Bgee_15_0"
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_0 was found in the download directory C:/Users/biocbuild/bbs-3.14-bioc/meat/BgeeDB.Rcheck/tests_x64/testthat. Data will not be redownloaded.
API key built: 7cb00f7734bc1341352a4181373b6d014a68f8e24c6893009a4ab69380c33b6f75c51647b6c4c725245acc6fa72ea5a9ace2aca6716b40621a41c039d28fe3d2
Saved annotation files in C:/Users/biocbuild/bbs-3.14-bioc/meat/BgeeDB.Rcheck/tests_x64/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 C:/Users/biocbuild/bbs-3.14-bioc/meat/BgeeDB.Rcheck/tests_x64/testthat. Data will not be redownloaded.
API key built: 7cb00f7734bc1341352a4181373b6d014a68f8e24c6893009a4ab69380c33b6f75c51647b6c4c725245acc6fa72ea5a9ace2aca6716b40621a41c039d28fe3d2
NOTE: annotation files for this species were found in the download directory C:/Users/biocbuild/bbs-3.14-bioc/meat/BgeeDB.Rcheck/tests_x64/testthat/Mus_musculus_Bgee_15_0. Data will not be redownloaded.
Querying Bgee to get release information...
NOTE: the file describing Bgee species information for release 15_0 was found in the download directory C:/Users/biocbuild/bbs-3.14-bioc/meat/BgeeDB.Rcheck/tests_x64/testthat. Data will not be redownloaded.
API key built: 7cb00f7734bc1341352a4181373b6d014a68f8e24c6893009a4ab69380c33b6f75c51647b6c4c725245acc6fa72ea5a9ace2aca6716b40621a41c039d28fe3d2
NOTE: an organ relationships file was found in the download directory C:/Users/biocbuild/bbs-3.14-bioc/meat/BgeeDB.Rcheck/tests_x64/testthat/Bos_taurus_Bgee_15_0. Data will not be redownloaded.
NOTE: an organ names file was found in the download directory C:/Users/biocbuild/bbs-3.14-bioc/meat/BgeeDB.Rcheck/tests_x64/testthat/Bos_taurus_Bgee_15_0. Data will not be redownloaded.
NOTE: a gene to organs mapping file was found in the download directory C:/Users/biocbuild/bbs-3.14-bioc/meat/BgeeDB.Rcheck/tests_x64/testthat/Bos_taurus_Bgee_15_0. 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 1 | SKIP 0 | PASS 32 ]
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 32 ]
>
> proc.time()
user system elapsed
38.45 2.85 153.98
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BgeeDB.Rcheck/examples_i386/BgeeDB-Ex.timings
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BgeeDB.Rcheck/examples_x64/BgeeDB-Ex.timings
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