Julien Wollbrett
| Snapshot Date: 2024-11-24 13:40 -0500 (Sun, 24 Nov 2024) |
| git_url: https://git.bioconductor.org/packages/BgeeDB |
| git_branch: devel |
| git_last_commit: 13c7c42 |
| git_last_commit_date: 2024-10-29 10:10:09 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2024-11-25 11:39 -0500 (Mon, 25 Nov 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4748 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4459 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4349 |
| 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 | ||||
| Package 163/2272 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BgeeDB 2.33.0 (landing page) Julien Wollbrett
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
|
To the developers/maintainers of the BgeeDB package: - 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 Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: BgeeDB |
| Version: 2.33.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BgeeDB.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BgeeDB_2.33.0.tar.gz |
| StartedAt: 2024-11-24 19:46:22 -0500 (Sun, 24 Nov 2024) |
| EndedAt: 2024-11-24 20:05:37 -0500 (Sun, 24 Nov 2024) |
| EllapsedTime: 1155.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BgeeDB.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BgeeDB.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BgeeDB_2.33.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/BgeeDB.Rcheck’
* using R Under development (unstable) (2024-11-20 r87352)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BgeeDB/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BgeeDB’ version ‘2.33.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘BgeeDB’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
makeTable 12.776 51.326 276.144
topAnat 6.648 16.911 89.322
geneList 12.402 0.553 68.182
getIntegratedCalls 3.499 4.286 64.611
deleteLocalData 3.689 0.363 8.415
loadTopAnatData 1.857 1.563 41.051
formatData 2.392 0.305 5.814
getData 1.060 0.457 5.657
getSampleProcessedData 1.107 0.252 6.554
listBgeeSpecies 0.086 0.029 10.659
Bgee-class 0.052 0.012 7.551
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: OK
BgeeDB.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL BgeeDB ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’ * installing *source* package ‘BgeeDB’ ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading groupGOTerms: GOBPTerm, GOMFTerm, GOCCTerm environments built. ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location groupGOTerms: GOBPTerm, GOMFTerm, GOCCTerm environments built. ** testing if installed package can be loaded from final location groupGOTerms: GOBPTerm, GOMFTerm, GOCCTerm environments built. ** testing if installed package keeps a record of temporary installation path * DONE (BgeeDB)
BgeeDB.Rcheck/tests/testthat.Rout
R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(BgeeDB)
Loading required package: topGO
Loading required package: BiocGenerics
Loading required package: generics
Attaching package: 'generics'
The following objects are masked from 'package:base':
as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
setequal, union
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
unsplit, which.max, which.min
Loading required package: graph
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: GO.db
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: IRanges
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:utils':
findMatches
The following objects are masked from 'package:base':
I, expand.grid, unname
Loading required package: SparseM
groupGOTerms: GOBPTerm, GOMFTerm, GOCCTerm environments built.
Attaching package: 'topGO'
The following object is masked from 'package:IRanges':
members
Loading required package: tidyr
Attaching package: 'tidyr'
The following object is masked from 'package:S4Vectors':
expand
The following object is masked from 'package:testthat':
matches
>
> Sys.setenv("R_TESTS" = "")
> test_check("BgeeDB")
Querying Bgee to get release information...
Building URL to query species in Bgee release 15_2...
downloading Bgee species info... (https://www.bgee.org/ftp/bgee_v15_2/rPackageSpeciesInfo.tsv)
Download of species information successful!
API key built: 59929df004fa90a3c0fdd680e629438bb7f60d31fdf81e257ed5772aefe97d9d8007cd23ff7f82fd143eb86aba004d2a4a9b37d6e68956477d32cf1d14dbd480
Saved annotation files in /Users/biocbuild/bbs-3.21-bioc/meat/BgeeDB.Rcheck/tests/testthat/Mus_musculus_Bgee_15_2 folder.
Extracting expression data matrix...
Keeping only present genes.
Extracting features information...
Extracting samples information...
Extracting expression data matrix...
Keeping only present genes.
Extracting features information...
Extracting samples information...
Querying Bgee to get release information...
Building URL to query species in Bgee release 13_2...
downloading Bgee species info... (https://r.bgee.org/bgee13/?page=species&display_type=tsv&source=BgeeDB_R_package&source_version=2.33.0)
Download of species information successful!
API key built: 59929df004fa90a3c0fdd680e629438bb7f60d31fdf81e257ed5772aefe97d9d8007cd23ff7f82fd143eb86aba004d2a4a9b37d6e68956477d32cf1d14dbd480
IMPORTANT INFORMATION: Be careful! You are not using the last release of the Bgee database! If it is not intentional you should update to the last version of Bioconductor and of the BgeeDB package. To update Bioconductor, see https://www.bioconductor.org/install/
Saved annotation files in /Users/biocbuild/bbs-3.21-bioc/meat/BgeeDB.Rcheck/tests/testthat/Mus_musculus_Bgee_13_2 folder.
Extracting expression data matrix...
Keeping only present genes.
Extracting features information...
Extracting samples information...
Extracting expression data matrix...
Keeping only present genes.
Extracting features information...
Extracting samples information...
Querying Bgee to get release information...
NOTE: the file describing Bgee species information for release 15_2 was found in the download directory /Users/biocbuild/bbs-3.21-bioc/meat/BgeeDB.Rcheck/tests/testthat. Data will not be redownloaded.
API key built: 59929df004fa90a3c0fdd680e629438bb7f60d31fdf81e257ed5772aefe97d9d8007cd23ff7f82fd143eb86aba004d2a4a9b37d6e68956477d32cf1d14dbd480
Querying Bgee to get release information...
NOTE: the file describing Bgee species information for release 15_2 was found in the download directory /Users/biocbuild/bbs-3.21-bioc/meat/BgeeDB.Rcheck/tests/testthat. Data will not be redownloaded.
API key built: 59929df004fa90a3c0fdd680e629438bb7f60d31fdf81e257ed5772aefe97d9d8007cd23ff7f82fd143eb86aba004d2a4a9b37d6e68956477d32cf1d14dbd480
Saved annotation files in /Users/biocbuild/bbs-3.21-bioc/meat/BgeeDB.Rcheck/tests/testthat/Mus_musculus_Bgee_15_2 folder.
Querying Bgee to get release information...
NOTE: the file describing Bgee species information for release 13_2 was found in the download directory /Users/biocbuild/bbs-3.21-bioc/meat/BgeeDB.Rcheck/tests/testthat. Data will not be redownloaded.
API key built: 59929df004fa90a3c0fdd680e629438bb7f60d31fdf81e257ed5772aefe97d9d8007cd23ff7f82fd143eb86aba004d2a4a9b37d6e68956477d32cf1d14dbd480
IMPORTANT INFORMATION: Be careful! You are not using the last release of the Bgee database! If it is not intentional you should update to the last version of Bioconductor and of the BgeeDB package. To update Bioconductor, see https://www.bioconductor.org/install/
Querying Bgee to get release information...
NOTE: the file describing Bgee species information for release 13_2 was found in the download directory /Users/biocbuild/bbs-3.21-bioc/meat/BgeeDB.Rcheck/tests/testthat. Data will not be redownloaded.
API key built: 59929df004fa90a3c0fdd680e629438bb7f60d31fdf81e257ed5772aefe97d9d8007cd23ff7f82fd143eb86aba004d2a4a9b37d6e68956477d32cf1d14dbd480
IMPORTANT INFORMATION: Be careful! You are not using the last release of the Bgee database! If it is not intentional you should update to the last version of Bioconductor and of the BgeeDB package. To update Bioconductor, see https://www.bioconductor.org/install/
Saved annotation files in /Users/biocbuild/bbs-3.21-bioc/meat/BgeeDB.Rcheck/tests/testthat/Mus_musculus_Bgee_13_2 folder.
Querying Bgee to get release information...
Building URL to query species in Bgee release 14_2...
downloading Bgee species info... (https://r.bgee.org/bgee14_2/?page=r_package&action=get_all_species&display_type=tsv&source=BgeeDB_R_package&source_version=2.33.0)
Download of species information successful!
Querying Bgee to get release information...
NOTE: the file describing Bgee species information for release 15_2 was found in the download directory /Users/biocbuild/bbs-3.21-bioc/meat/BgeeDB.Rcheck/tests/testthat. Data will not be redownloaded.
API key built: 59929df004fa90a3c0fdd680e629438bb7f60d31fdf81e257ed5772aefe97d9d8007cd23ff7f82fd143eb86aba004d2a4a9b37d6e68956477d32cf1d14dbd480
Building URLs to retrieve organ relationships from Bgee.........
URL successfully built (https://www.bgee.org/bgee15_2/api/?page=r_package&action=get_anat_entity_relations&display_type=tsv&species_list=9913&attr_list=SOURCE_ID&attr_list=TARGET_ID&api_key=59929df004fa90a3c0fdd680e629438bb7f60d31fdf81e257ed5772aefe97d9d8007cd23ff7f82fd143eb86aba004d2a4a9b37d6e68956477d32cf1d14dbd480&source=BgeeDB_R_package&source_version=2.33.0)
Submitting URL to Bgee webservice (can be long)
Got results from Bgee webservice. Files are written in "/Users/biocbuild/bbs-3.21-bioc/meat/BgeeDB.Rcheck/tests/testthat/Bos_taurus_Bgee_15_2"
Building URLs to retrieve organ names from Bgee.................
URL successfully built (https://www.bgee.org/bgee15_2/api/?page=r_package&action=get_anat_entities&display_type=tsv&species_list=9913&attr_list=ID&attr_list=NAME&api_key=59929df004fa90a3c0fdd680e629438bb7f60d31fdf81e257ed5772aefe97d9d8007cd23ff7f82fd143eb86aba004d2a4a9b37d6e68956477d32cf1d14dbd480&source=BgeeDB_R_package&source_version=2.33.0)
Submitting URL to Bgee webservice (can be long)
Got results from Bgee webservice. Files are written in "/Users/biocbuild/bbs-3.21-bioc/meat/BgeeDB.Rcheck/tests/testthat/Bos_taurus_Bgee_15_2"
Building URLs to retrieve mapping of gene to organs from Bgee...
URL successfully built (https://www.bgee.org/bgee15_2/api/?page=r_package&action=get_expression_calls&display_type=tsv&species_list=9913&attr_list=GENE_ID&attr_list=ANAT_ENTITY_ID&api_key=59929df004fa90a3c0fdd680e629438bb7f60d31fdf81e257ed5772aefe97d9d8007cd23ff7f82fd143eb86aba004d2a4a9b37d6e68956477d32cf1d14dbd480&source=BgeeDB_R_package&source_version=2.33.0&data_type=RNA_SEQ&data_qual=SILVER&stage_id=UBERON:0000092)
Submitting URL to Bgee webservice (can be long)
Got results from Bgee webservice. Files are written in "/Users/biocbuild/bbs-3.21-bioc/meat/BgeeDB.Rcheck/tests/testthat/Bos_taurus_Bgee_15_2"
Parsing the results.............................................
Adding BGEE:0 as unique root of all terms of the ontology.......
Done.
Querying Bgee to get release information...
NOTE: the file describing Bgee species information for release 15_2 was found in the download directory /Users/biocbuild/bbs-3.21-bioc/meat/BgeeDB.Rcheck/tests/testthat. Data will not be redownloaded.
API key built: 59929df004fa90a3c0fdd680e629438bb7f60d31fdf81e257ed5772aefe97d9d8007cd23ff7f82fd143eb86aba004d2a4a9b37d6e68956477d32cf1d14dbd480
Saved annotation files in /Users/biocbuild/bbs-3.21-bioc/meat/BgeeDB.Rcheck/tests/testthat/Drosophila_simulans_Bgee_15_2 folder.
Querying Bgee to get release information...
NOTE: the file describing Bgee species information for release 15_2 was found in the download directory /Users/biocbuild/bbs-3.21-bioc/meat/BgeeDB.Rcheck/tests/testthat. Data will not be redownloaded.
API key built: 59929df004fa90a3c0fdd680e629438bb7f60d31fdf81e257ed5772aefe97d9d8007cd23ff7f82fd143eb86aba004d2a4a9b37d6e68956477d32cf1d14dbd480
Querying Bgee to get release information...
NOTE: the file describing Bgee species information for release 15_2 was found in the download directory /Users/biocbuild/bbs-3.21-bioc/meat/BgeeDB.Rcheck/tests/testthat. Data will not be redownloaded.
API key built: 59929df004fa90a3c0fdd680e629438bb7f60d31fdf81e257ed5772aefe97d9d8007cd23ff7f82fd143eb86aba004d2a4a9b37d6e68956477d32cf1d14dbd480
NOTE: an organ relationships file was found in the download directory /Users/biocbuild/bbs-3.21-bioc/meat/BgeeDB.Rcheck/tests/testthat/Bos_taurus_Bgee_15_2. Data will not be redownloaded.
NOTE: an organ names file was found in the download directory /Users/biocbuild/bbs-3.21-bioc/meat/BgeeDB.Rcheck/tests/testthat/Bos_taurus_Bgee_15_2. Data will not be redownloaded.
NOTE: a gene to organs mapping file was found in the download directory /Users/biocbuild/bbs-3.21-bioc/meat/BgeeDB.Rcheck/tests/testthat/Bos_taurus_Bgee_15_2. Data will not be redownloaded.
Parsing the results.............................................
Adding BGEE:0 as unique root of all terms of the ontology.......
Done.
Checking topAnatData object.............
Checking gene list......................
WARNING: Some genes in your gene list have no expression data in Bgee, and will not be included in the analysis. 98 genes in background will be kept.
Building most specific Ontology terms... ( 110 Ontology terms found. )
Building DAG topology................... ( 549 Ontology terms and 994 relations. )
Annotating nodes (Can be long).......... ( 95 genes annotated to the Ontology terms. )
[ FAIL 0 | WARN 8 | SKIP 0 | PASS 32 ]
[ FAIL 0 | WARN 8 | SKIP 0 | PASS 32 ]
>
> proc.time()
user system elapsed
34.568 6.542 149.424
BgeeDB.Rcheck/BgeeDB-Ex.timings
| name | user | system | elapsed | |
| Bgee-class | 0.052 | 0.012 | 7.551 | |
| deleteLocalData | 3.689 | 0.363 | 8.415 | |
| deleteOldData | 0.017 | 0.004 | 0.423 | |
| formatData | 2.392 | 0.305 | 5.814 | |
| geneList | 12.402 | 0.553 | 68.182 | |
| getAnnotation | 0.050 | 0.021 | 0.629 | |
| getCellProcessedData | 0 | 0 | 0 | |
| getData | 1.060 | 0.457 | 5.657 | |
| getIntegratedCalls | 3.499 | 4.286 | 64.611 | |
| getSampleProcessedData | 1.107 | 0.252 | 6.554 | |
| listBgeeRelease | 0.015 | 0.006 | 0.372 | |
| listBgeeSpecies | 0.086 | 0.029 | 10.659 | |
| loadTopAnatData | 1.857 | 1.563 | 41.051 | |
| makeTable | 12.776 | 51.326 | 276.144 | |
| topAnat | 6.648 | 16.911 | 89.322 | |