Back to Multiple platform build/check report for BioC 3.13
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This page was generated on 2021-08-02 15:05:05 -0400 (Mon, 02 Aug 2021).

CHECK results for BgeeDB on tokay2

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? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 143/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BgeeDB 2.18.1  (landing page)
Julien Wollbrett , Julien Roux , Andrea Komljenovic , Frederic Bastian
Snapshot Date: 2021-08-01 04:50:10 -0400 (Sun, 01 Aug 2021)
URL: https://git.bioconductor.org/packages/BgeeDB
Branch: RELEASE_3_13
Last Commit: 6e3f28d
Last Changed Date: 2021-06-15 22:49:49 -0400 (Tue, 15 Jun 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: BgeeDB
Version: 2.18.1
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BgeeDB.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings BgeeDB_2.18.1.tar.gz
StartedAt: 2021-08-01 20:14:40 -0400 (Sun, 01 Aug 2021)
EndedAt: 2021-08-01 20:30:57 -0400 (Sun, 01 Aug 2021)
EllapsedTime: 976.6 seconds
RetCode: 0
Status:   OK  
CheckDir: BgeeDB.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BgeeDB.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings BgeeDB_2.18.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/BgeeDB.Rcheck'
* using R version 4.1.0 (2021-05-18)
* 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 '2.18.1'
* 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
makeTable       12.22   0.94   59.41
geneList        11.68   0.97   58.74
loadTopAnatData  8.00   0.64  101.90
topAnat          7.56   0.62    9.05
formatData       5.24   0.77   11.65
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
geneList        12.49   0.58   40.34
makeTable       11.35   0.88   59.36
loadTopAnatData  8.28   0.51   86.62
topAnat          6.32   0.67    7.88
formatData       4.86   0.73   11.22
* 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


Installation output

BgeeDB.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/BgeeDB_2.18.1.tar.gz && rm -rf BgeeDB.buildbin-libdir && mkdir BgeeDB.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=BgeeDB.buildbin-libdir BgeeDB_2.18.1.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL BgeeDB_2.18.1.zip && rm BgeeDB_2.18.1.tar.gz BgeeDB_2.18.1.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  9 70391    9  6538    0     0   115k      0 --:--:-- --:--:-- --:--:--  116k
100 70391  100 70391    0     0   684k      0 --:--:-- --:--:-- --:--:--  687k

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_2.18.1.zip
* DONE (BgeeDB)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'BgeeDB' successfully unpacked and MD5 sums checked

Tests output

BgeeDB.Rcheck/tests_i386/testthat.Rout


R version 4.1.0 (2021-05-18) -- "Camp Pontanezen"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(BgeeDB)
Loading required package: topGO
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: graph
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: GO.db
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following 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/?page=r_package&action=get_all_species&display_type=tsv&source=BgeeDB_R_package&source_version=2.18.1)

Query to Bgee webservice successful!

API key built: 0d95e34ad58732256361ccd2aa69fd53e099fc962f7a3af16c157a2ba2213ca47dd765baa8ec9a3e9b8f98852c23ce18c4606b7c8b3fdf74c6586eb0728201bd

Saved annotation files in C:/Users/biocbuild/bbs-3.13-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=2.18.1)

Query to Bgee webservice successful!

API key built: 0d95e34ad58732256361ccd2aa69fd53e099fc962f7a3af16c157a2ba2213ca47dd765baa8ec9a3e9b8f98852c23ce18c4606b7c8b3fdf74c6586eb0728201bd

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-3.13-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-3.13-bioc/meat/BgeeDB.Rcheck/tests_i386/testthat. Data will not be redownloaded.

API key built: 0d95e34ad58732256361ccd2aa69fd53e099fc962f7a3af16c157a2ba2213ca47dd765baa8ec9a3e9b8f98852c23ce18c4606b7c8b3fdf74c6586eb0728201bd

NOTE: annotation files for this species were found in the download directory C:/Users/biocbuild/bbs-3.13-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-3.13-bioc/meat/BgeeDB.Rcheck/tests_i386/testthat. Data will not be redownloaded.

API key built: 0d95e34ad58732256361ccd2aa69fd53e099fc962f7a3af16c157a2ba2213ca47dd765baa8ec9a3e9b8f98852c23ce18c4606b7c8b3fdf74c6586eb0728201bd

Saved annotation files in C:/Users/biocbuild/bbs-3.13-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-3.13-bioc/meat/BgeeDB.Rcheck/tests_i386/testthat. Data will not be redownloaded.

API key built: 0d95e34ad58732256361ccd2aa69fd53e099fc962f7a3af16c157a2ba2213ca47dd765baa8ec9a3e9b8f98852c23ce18c4606b7c8b3fdf74c6586eb0728201bd

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-3.13-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-3.13-bioc/meat/BgeeDB.Rcheck/tests_i386/testthat. Data will not be redownloaded.

API key built: 0d95e34ad58732256361ccd2aa69fd53e099fc962f7a3af16c157a2ba2213ca47dd765baa8ec9a3e9b8f98852c23ce18c4606b7c8b3fdf74c6586eb0728201bd

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-3.13-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=2.18.1)

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-3.13-bioc/meat/BgeeDB.Rcheck/tests_i386/testthat. Data will not be redownloaded.

API key built: 0d95e34ad58732256361ccd2aa69fd53e099fc962f7a3af16c157a2ba2213ca47dd765baa8ec9a3e9b8f98852c23ce18c4606b7c8b3fdf74c6586eb0728201bd

Building URLs to retrieve organ relationships from Bgee.........
   URL successfully built (https://bgee.org/bgee15_0/?page=r_package&action=get_anat_entity_relations&display_type=tsv&species_list=9913&attr_list=SOURCE_ID&attr_list=TARGET_ID&api_key=0d95e34ad58732256361ccd2aa69fd53e099fc962f7a3af16c157a2ba2213ca47dd765baa8ec9a3e9b8f98852c23ce18c4606b7c8b3fdf74c6586eb0728201bd&source=BgeeDB_R_package&source_version=2.18.1)
   Submitting URL to Bgee webservice (can be long)
   Got results from Bgee webservice. Files are written in "C:/Users/biocbuild/bbs-3.13-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/?page=r_package&action=get_anat_entities&display_type=tsv&species_list=9913&attr_list=ID&attr_list=NAME&api_key=0d95e34ad58732256361ccd2aa69fd53e099fc962f7a3af16c157a2ba2213ca47dd765baa8ec9a3e9b8f98852c23ce18c4606b7c8b3fdf74c6586eb0728201bd&source=BgeeDB_R_package&source_version=2.18.1)
   Submitting URL to Bgee webservice (can be long)
   Got results from Bgee webservice. Files are written in "C:/Users/biocbuild/bbs-3.13-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/?page=r_package&action=get_expression_calls&display_type=tsv&species_list=9913&attr_list=GENE_ID&attr_list=ANAT_ENTITY_ID&api_key=0d95e34ad58732256361ccd2aa69fd53e099fc962f7a3af16c157a2ba2213ca47dd765baa8ec9a3e9b8f98852c23ce18c4606b7c8b3fdf74c6586eb0728201bd&source=BgeeDB_R_package&source_version=2.18.1&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-3.13-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-3.13-bioc/meat/BgeeDB.Rcheck/tests_i386/testthat. Data will not be redownloaded.

API key built: 0d95e34ad58732256361ccd2aa69fd53e099fc962f7a3af16c157a2ba2213ca47dd765baa8ec9a3e9b8f98852c23ce18c4606b7c8b3fdf74c6586eb0728201bd

Saved annotation files in C:/Users/biocbuild/bbs-3.13-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-3.13-bioc/meat/BgeeDB.Rcheck/tests_i386/testthat. Data will not be redownloaded.

API key built: 0d95e34ad58732256361ccd2aa69fd53e099fc962f7a3af16c157a2ba2213ca47dd765baa8ec9a3e9b8f98852c23ce18c4606b7c8b3fdf74c6586eb0728201bd

NOTE: annotation files for this species were found in the download directory C:/Users/biocbuild/bbs-3.13-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-3.13-bioc/meat/BgeeDB.Rcheck/tests_i386/testthat. Data will not be redownloaded.

API key built: 0d95e34ad58732256361ccd2aa69fd53e099fc962f7a3af16c157a2ba2213ca47dd765baa8ec9a3e9b8f98852c23ce18c4606b7c8b3fdf74c6586eb0728201bd

NOTE: an organ relationships file was found in the download directory C:/Users/biocbuild/bbs-3.13-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-3.13-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-3.13-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...  (  111  Ontology terms found. )

Building DAG topology...................  (  551  Ontology terms and  996  relations. )

Annotating nodes (Can be long)..........  (  95  genes annotated to the Ontology terms. )
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 32 ]
Warning message:
call dbDisconnect() when finished working with a connection 
> 
> proc.time()
   user  system elapsed 
  39.98    3.82  148.32 

BgeeDB.Rcheck/tests_x64/testthat.Rout


R version 4.1.0 (2021-05-18) -- "Camp Pontanezen"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(BgeeDB)
Loading required package: topGO
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: graph
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: GO.db
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following 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/?page=r_package&action=get_all_species&display_type=tsv&source=BgeeDB_R_package&source_version=2.18.1)

Query to Bgee webservice successful!

API key built: 3474650028ba8809396ae02af32a8a91bbe8c450c0e6105a6dbd57d5505c6be18a247bd3a369be7bfd191724b1c029924933386f1067d55cd88d42bbc113711e

Saved annotation files in C:/Users/biocbuild/bbs-3.13-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=2.18.1)

Query to Bgee webservice successful!

API key built: 3474650028ba8809396ae02af32a8a91bbe8c450c0e6105a6dbd57d5505c6be18a247bd3a369be7bfd191724b1c029924933386f1067d55cd88d42bbc113711e

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-3.13-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-3.13-bioc/meat/BgeeDB.Rcheck/tests_x64/testthat. Data will not be redownloaded.

API key built: 3474650028ba8809396ae02af32a8a91bbe8c450c0e6105a6dbd57d5505c6be18a247bd3a369be7bfd191724b1c029924933386f1067d55cd88d42bbc113711e

NOTE: annotation files for this species were found in the download directory C:/Users/biocbuild/bbs-3.13-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-3.13-bioc/meat/BgeeDB.Rcheck/tests_x64/testthat. Data will not be redownloaded.

API key built: 3474650028ba8809396ae02af32a8a91bbe8c450c0e6105a6dbd57d5505c6be18a247bd3a369be7bfd191724b1c029924933386f1067d55cd88d42bbc113711e

Saved annotation files in C:/Users/biocbuild/bbs-3.13-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-3.13-bioc/meat/BgeeDB.Rcheck/tests_x64/testthat. Data will not be redownloaded.

API key built: 3474650028ba8809396ae02af32a8a91bbe8c450c0e6105a6dbd57d5505c6be18a247bd3a369be7bfd191724b1c029924933386f1067d55cd88d42bbc113711e

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-3.13-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-3.13-bioc/meat/BgeeDB.Rcheck/tests_x64/testthat. Data will not be redownloaded.

API key built: 3474650028ba8809396ae02af32a8a91bbe8c450c0e6105a6dbd57d5505c6be18a247bd3a369be7bfd191724b1c029924933386f1067d55cd88d42bbc113711e

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-3.13-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=2.18.1)

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-3.13-bioc/meat/BgeeDB.Rcheck/tests_x64/testthat. Data will not be redownloaded.

API key built: 3474650028ba8809396ae02af32a8a91bbe8c450c0e6105a6dbd57d5505c6be18a247bd3a369be7bfd191724b1c029924933386f1067d55cd88d42bbc113711e

Building URLs to retrieve organ relationships from Bgee.........
   URL successfully built (https://bgee.org/bgee15_0/?page=r_package&action=get_anat_entity_relations&display_type=tsv&species_list=9913&attr_list=SOURCE_ID&attr_list=TARGET_ID&api_key=3474650028ba8809396ae02af32a8a91bbe8c450c0e6105a6dbd57d5505c6be18a247bd3a369be7bfd191724b1c029924933386f1067d55cd88d42bbc113711e&source=BgeeDB_R_package&source_version=2.18.1)
   Submitting URL to Bgee webservice (can be long)
   Got results from Bgee webservice. Files are written in "C:/Users/biocbuild/bbs-3.13-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/?page=r_package&action=get_anat_entities&display_type=tsv&species_list=9913&attr_list=ID&attr_list=NAME&api_key=3474650028ba8809396ae02af32a8a91bbe8c450c0e6105a6dbd57d5505c6be18a247bd3a369be7bfd191724b1c029924933386f1067d55cd88d42bbc113711e&source=BgeeDB_R_package&source_version=2.18.1)
   Submitting URL to Bgee webservice (can be long)
   Got results from Bgee webservice. Files are written in "C:/Users/biocbuild/bbs-3.13-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/?page=r_package&action=get_expression_calls&display_type=tsv&species_list=9913&attr_list=GENE_ID&attr_list=ANAT_ENTITY_ID&api_key=3474650028ba8809396ae02af32a8a91bbe8c450c0e6105a6dbd57d5505c6be18a247bd3a369be7bfd191724b1c029924933386f1067d55cd88d42bbc113711e&source=BgeeDB_R_package&source_version=2.18.1&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-3.13-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-3.13-bioc/meat/BgeeDB.Rcheck/tests_x64/testthat. Data will not be redownloaded.

API key built: 3474650028ba8809396ae02af32a8a91bbe8c450c0e6105a6dbd57d5505c6be18a247bd3a369be7bfd191724b1c029924933386f1067d55cd88d42bbc113711e

Saved annotation files in C:/Users/biocbuild/bbs-3.13-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-3.13-bioc/meat/BgeeDB.Rcheck/tests_x64/testthat. Data will not be redownloaded.

API key built: 3474650028ba8809396ae02af32a8a91bbe8c450c0e6105a6dbd57d5505c6be18a247bd3a369be7bfd191724b1c029924933386f1067d55cd88d42bbc113711e

NOTE: annotation files for this species were found in the download directory C:/Users/biocbuild/bbs-3.13-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-3.13-bioc/meat/BgeeDB.Rcheck/tests_x64/testthat. Data will not be redownloaded.

API key built: 3474650028ba8809396ae02af32a8a91bbe8c450c0e6105a6dbd57d5505c6be18a247bd3a369be7bfd191724b1c029924933386f1067d55cd88d42bbc113711e

NOTE: an organ relationships file was found in the download directory C:/Users/biocbuild/bbs-3.13-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-3.13-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-3.13-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...  (  111  Ontology terms found. )

Building DAG topology...................  (  551  Ontology terms and  996  relations. )

Annotating nodes (Can be long)..........  (  95  genes annotated to the Ontology terms. )
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 32 ]
Warning message:
call dbDisconnect() when finished working with a connection 
> 
> proc.time()
   user  system elapsed 
  34.50    3.31  180.98 

Example timings

BgeeDB.Rcheck/examples_i386/BgeeDB-Ex.timings

nameusersystemelapsed
Bgee-class0.250.002.78
deleteLocalData0.040.000.67
deleteOldData0.010.000.66
formatData 5.24 0.7711.65
geneList11.68 0.9758.74
getAnnotation0.040.010.67
getData1.770.172.57
listBgeeRelease0.010.020.68
listBgeeSpecies0.080.003.17
loadTopAnatData 8.00 0.64101.90
makeTable12.22 0.9459.41
topAnat7.560.629.05

BgeeDB.Rcheck/examples_x64/BgeeDB-Ex.timings

nameusersystemelapsed
Bgee-class0.080.002.48
deleteLocalData0.030.000.67
deleteOldData0.010.000.66
formatData 4.86 0.7311.22
geneList12.49 0.5840.34
getAnnotation0.030.000.69
getData1.530.202.36
listBgeeRelease0.000.020.65
listBgeeSpecies0.060.003.19
loadTopAnatData 8.28 0.5186.62
makeTable11.35 0.8859.36
topAnat6.320.677.88