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CHECK report for BgeeDB on machv2

This page was generated on 2020-10-17 11:58:06 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE BgeeDB PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 138/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BgeeDB 2.14.5
Julien Wollbrett , Julien Roux , Andrea Komljenovic , Frederic Bastian
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/BgeeDB
Branch: RELEASE_3_11
Last Commit: 01114bd
Last Changed Date: 2020-06-04 05:12:44 -0400 (Thu, 04 Jun 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: BgeeDB
Version: 2.14.5
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:BgeeDB.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings BgeeDB_2.14.5.tar.gz
StartedAt: 2020-10-16 22:59:25 -0400 (Fri, 16 Oct 2020)
EndedAt: 2020-10-16 23:15:42 -0400 (Fri, 16 Oct 2020)
EllapsedTime: 977.0 seconds
RetCode: 0
Status:  OK 
CheckDir: BgeeDB.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:BgeeDB.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings BgeeDB_2.14.5.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/BgeeDB.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BgeeDB/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BgeeDB’ version ‘2.14.5’
* 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 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 R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... 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
getData         465.855 39.245 575.849
geneList         17.152  0.624  51.362
formatData        5.228  0.346  12.363
makeTable         3.145  0.237   9.084
loadTopAnatData   2.275  0.211  36.349
listBgeeSpecies   0.111  0.024   9.205
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: OK

Installation output

BgeeDB.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL BgeeDB
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/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)

Tests output

BgeeDB.Rcheck/tests/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-apple-darwin17.0 (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


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: ee768c0348f90b6271d03c1a97fde3383c4203fb24b6394e6005e470280ddf6e1a9b09feb4109017a9f6ed4e3cfd17026714458d6f7f6ebd1418fb8d5056bab3

Saved annotation files in /Users/biocbuild/bbs-3.11-bioc/meat/BgeeDB.Rcheck/tests/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: ee768c0348f90b6271d03c1a97fde3383c4203fb24b6394e6005e470280ddf6e1a9b09feb4109017a9f6ed4e3cfd17026714458d6f7f6ebd1418fb8d5056bab3

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-3.11-bioc/meat/BgeeDB.Rcheck/tests/testthat/Mus_musculus_Bgee_13_2 folder.

Extracting expression data matrix...
  Keeping only present genes.

Extracting features information...

Extracting samples information...

Extracting expression data matrix...
  Keeping only present genes.

Extracting features information...

Extracting samples information...

Querying Bgee to get release information...

NOTE: the file describing Bgee species information for release 14_1 was found in the download directory /Users/biocbuild/bbs-3.11-bioc/meat/BgeeDB.Rcheck/tests/testthat. Data will not be redownloaded.

API key built: ee768c0348f90b6271d03c1a97fde3383c4203fb24b6394e6005e470280ddf6e1a9b09feb4109017a9f6ed4e3cfd17026714458d6f7f6ebd1418fb8d5056bab3

NOTE: annotation files for this species were found in the download directory /Users/biocbuild/bbs-3.11-bioc/meat/BgeeDB.Rcheck/tests/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 /Users/biocbuild/bbs-3.11-bioc/meat/BgeeDB.Rcheck/tests/testthat. Data will not be redownloaded.

API key built: ee768c0348f90b6271d03c1a97fde3383c4203fb24b6394e6005e470280ddf6e1a9b09feb4109017a9f6ed4e3cfd17026714458d6f7f6ebd1418fb8d5056bab3

Saved annotation files in /Users/biocbuild/bbs-3.11-bioc/meat/BgeeDB.Rcheck/tests/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 /Users/biocbuild/bbs-3.11-bioc/meat/BgeeDB.Rcheck/tests/testthat. Data will not be redownloaded.

API key built: ee768c0348f90b6271d03c1a97fde3383c4203fb24b6394e6005e470280ddf6e1a9b09feb4109017a9f6ed4e3cfd17026714458d6f7f6ebd1418fb8d5056bab3

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 /Users/biocbuild/bbs-3.11-bioc/meat/BgeeDB.Rcheck/tests/testthat/Mus_musculus_Bgee_13_2. Data will not be redownloaded.

Querying Bgee to get release information...

NOTE: the file describing Bgee species information for release 13_2 was found in the download directory /Users/biocbuild/bbs-3.11-bioc/meat/BgeeDB.Rcheck/tests/testthat. Data will not be redownloaded.

API key built: ee768c0348f90b6271d03c1a97fde3383c4203fb24b6394e6005e470280ddf6e1a9b09feb4109017a9f6ed4e3cfd17026714458d6f7f6ebd1418fb8d5056bab3

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-3.11-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_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: ee768c0348f90b6271d03c1a97fde3383c4203fb24b6394e6005e470280ddf6e1a9b09feb4109017a9f6ed4e3cfd17026714458d6f7f6ebd1418fb8d5056bab3

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=ee768c0348f90b6271d03c1a97fde3383c4203fb24b6394e6005e470280ddf6e1a9b09feb4109017a9f6ed4e3cfd17026714458d6f7f6ebd1418fb8d5056bab3&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 "/Users/biocbuild/bbs-3.11-bioc/meat/BgeeDB.Rcheck/tests/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=ee768c0348f90b6271d03c1a97fde3383c4203fb24b6394e6005e470280ddf6e1a9b09feb4109017a9f6ed4e3cfd17026714458d6f7f6ebd1418fb8d5056bab3&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 "/Users/biocbuild/bbs-3.11-bioc/meat/BgeeDB.Rcheck/tests/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=ee768c0348f90b6271d03c1a97fde3383c4203fb24b6394e6005e470280ddf6e1a9b09feb4109017a9f6ed4e3cfd17026714458d6f7f6ebd1418fb8d5056bab3&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 "/Users/biocbuild/bbs-3.11-bioc/meat/BgeeDB.Rcheck/tests/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 /Users/biocbuild/bbs-3.11-bioc/meat/BgeeDB.Rcheck/tests/testthat. Data will not be redownloaded.

API key built: ee768c0348f90b6271d03c1a97fde3383c4203fb24b6394e6005e470280ddf6e1a9b09feb4109017a9f6ed4e3cfd17026714458d6f7f6ebd1418fb8d5056bab3

Saved annotation files in /Users/biocbuild/bbs-3.11-bioc/meat/BgeeDB.Rcheck/tests/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 /Users/biocbuild/bbs-3.11-bioc/meat/BgeeDB.Rcheck/tests/testthat. Data will not be redownloaded.

API key built: ee768c0348f90b6271d03c1a97fde3383c4203fb24b6394e6005e470280ddf6e1a9b09feb4109017a9f6ed4e3cfd17026714458d6f7f6ebd1418fb8d5056bab3

NOTE: annotation files for this species were found in the download directory /Users/biocbuild/bbs-3.11-bioc/meat/BgeeDB.Rcheck/tests/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 /Users/biocbuild/bbs-3.11-bioc/meat/BgeeDB.Rcheck/tests/testthat. Data will not be redownloaded.

API key built: ee768c0348f90b6271d03c1a97fde3383c4203fb24b6394e6005e470280ddf6e1a9b09feb4109017a9f6ed4e3cfd17026714458d6f7f6ebd1418fb8d5056bab3

NOTE: an organ relationships file was found in the download directory /Users/biocbuild/bbs-3.11-bioc/meat/BgeeDB.Rcheck/tests/testthat/Bos_taurus_Bgee_14_1. Data will not be redownloaded.

NOTE: an organ names file was found in the download directory /Users/biocbuild/bbs-3.11-bioc/meat/BgeeDB.Rcheck/tests/testthat/Bos_taurus_Bgee_14_1. Data will not be redownloaded.

NOTE: a gene to organs mapping file was found in the download directory /Users/biocbuild/bbs-3.11-bioc/meat/BgeeDB.Rcheck/tests/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 
 30.405   2.027 108.178

Example timings

BgeeDB.Rcheck/BgeeDB-Ex.timings

nameusersystemelapsed
Bgee-class0.1270.0134.358
deleteLocalData0.0160.0031.584
deleteOldData0.0170.0041.683
formatData 5.228 0.34612.363
geneList17.152 0.62451.362
getAnnotation0.0240.0051.720
getData465.855 39.245575.849
listBgeeRelease0.0090.0041.647
listBgeeSpecies0.1110.0249.205
loadTopAnatData 2.275 0.21136.349
makeTable3.1450.2379.084
topAnat2.1120.0744.474