Package: BgeeDB

Version: 2.12.1

Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:BgeeDB.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings BgeeDB_2.12.1.tar.gz

StartedAt: 2020-04-15 03:46:58 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 04:03:15 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 976.3 seconds

RetCode: 0

Status:  OK

CheckDir: BgeeDB.Rcheck

Warnings: 0

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### Running command:
###
###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:BgeeDB.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings BgeeDB_2.12.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/BgeeDB.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-pc-linux-gnu (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 ‘2.12.1’
* 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 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 ... NOTE
Malformed Title field: should not end in a period.
* checking top-level files ... NOTE
File
  LICENSE
is not mentioned in the DESCRIPTION file.
* 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 or elapsed time > 5s
                   user system elapsed
getData         224.540 12.668 241.969
geneList         13.824  0.252  41.421
loadTopAnatData   8.540  0.392 169.127
makeTable         7.444  0.084   9.901
topAnat           5.772  0.040   8.688
formatData        3.148  0.228   7.537
listBgeeSpecies   0.524  0.032   8.522
* 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.10-bioc/meat/BgeeDB.Rcheck/00check.log’
for details.

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### Running command:
###
###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL BgeeDB
###
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* installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/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)

R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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=2.12.1)
trying URL 'https://r.bgee.org/bgee14_1/?page=r_package&action=get_all_species&display_type=tsv&source=BgeeDB_R_package&source_version=2.12.1'
downloaded 1164 bytes


Query to Bgee webservice successful!

API key built: 9603140cd6217ac0b3d9cb71239dfda27da675c06e9090f5dd2ca55fc108cc124c874768b1ff88b7ff000ed70aa126d99741dc6b2ddb603ad2f3c64fb1e81445
trying URL 'ftp://ftp.bgee.org/bgee_v14_1/download/processed_expr_values/rna_seq/Mus_musculus/Mus_musculus_RNA-Seq_read_counts_TPM_FPKM_GSE43721.tsv.tar.gz'
Content type 'unknown' length 1866392 bytes (1.8 MB)
==================================================

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=2.12.1)
trying URL 'https://r.bgee.org/bgee13/?page=species&display_type=tsv&source=BgeeDB_R_package&source_version=2.12.1'
downloaded 707 bytes


Query to Bgee webservice successful!

API key built: 9603140cd6217ac0b3d9cb71239dfda27da675c06e9090f5dd2ca55fc108cc124c874768b1ff88b7ff000ed70aa126d99741dc6b2ddb603ad2f3c64fb1e81445

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/
trying URL 'ftp://ftp.bgee.org/bgee_v13_2/download/processed_expr_values/rna_seq/Mus_musculus/Mus_musculus_RNA-Seq_read_counts_RPKM_GSE43721.tsv.zip'
Content type 'unknown' length 919661 bytes (898 KB)
==================================================

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 /home/biocbuild/bbs-3.10-bioc/meat/BgeeDB.Rcheck/tests/testthat. Data will not be redownloaded.

API key built: 9603140cd6217ac0b3d9cb71239dfda27da675c06e9090f5dd2ca55fc108cc124c874768b1ff88b7ff000ed70aa126d99741dc6b2ddb603ad2f3c64fb1e81445
trying URL 'ftp://ftp.bgee.org/bgee_v14_1/download/processed_expr_values/rna_seq/Mus_musculus/Mus_musculus_RNA-Seq_experiments_libraries.tar.gz'
Content type 'unknown' length 28268 bytes (27 KB)
==================================================

Saved annotation files in /home/biocbuild/bbs-3.10-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 14_1 was found in the download directory /home/biocbuild/bbs-3.10-bioc/meat/BgeeDB.Rcheck/tests/testthat. Data will not be redownloaded.

API key built: 9603140cd6217ac0b3d9cb71239dfda27da675c06e9090f5dd2ca55fc108cc124c874768b1ff88b7ff000ed70aa126d99741dc6b2ddb603ad2f3c64fb1e81445
trying URL 'ftp://ftp.bgee.org/bgee_v14_1/download/processed_expr_values/affymetrix/Mus_musculus/Mus_musculus_Affymetrix_experiments_chips.tar.gz'
Content type 'unknown' length 512843 bytes (500 KB)
==================================================

Saved annotation files in /home/biocbuild/bbs-3.10-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 /home/biocbuild/bbs-3.10-bioc/meat/BgeeDB.Rcheck/tests/testthat. Data will not be redownloaded.

API key built: 9603140cd6217ac0b3d9cb71239dfda27da675c06e9090f5dd2ca55fc108cc124c874768b1ff88b7ff000ed70aa126d99741dc6b2ddb603ad2f3c64fb1e81445

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/
trying URL 'ftp://ftp.bgee.org/bgee_v13_2/download/processed_expr_values/rna_seq/Mus_musculus/Mus_musculus_RNA-Seq_experiments_libraries.zip'
Content type 'unknown' length 9379 bytes
==================================================

Saved annotation files in /home/biocbuild/bbs-3.10-bioc/meat/BgeeDB.Rcheck/tests/testthat/Mus_musculus_Bgee_13_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 /home/biocbuild/bbs-3.10-bioc/meat/BgeeDB.Rcheck/tests/testthat. Data will not be redownloaded.

API key built: 9603140cd6217ac0b3d9cb71239dfda27da675c06e9090f5dd2ca55fc108cc124c874768b1ff88b7ff000ed70aa126d99741dc6b2ddb603ad2f3c64fb1e81445

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/
trying URL 'ftp://ftp.bgee.org/bgee_v13_2/download/processed_expr_values/affymetrix/Mus_musculus/Mus_musculus_Affymetrix_experiments_chips.zip'
Content type 'unknown' length 500591 bytes (488 KB)
==================================================

Saved annotation files in /home/biocbuild/bbs-3.10-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=2.12.1)
trying URL 'https://r.bgee.org/bgee14_1/?page=r_package&action=get_all_species&display_type=tsv&source=BgeeDB_R_package&source_version=2.12.1'
downloaded 1164 bytes


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=2.12.1)
trying URL 'https://r.bgee.org/bgee14_1/?page=r_package&action=get_all_species&display_type=tsv&source=BgeeDB_R_package&source_version=2.12.1'
downloaded 1164 bytes


Query to Bgee webservice successful!

API key built: 9603140cd6217ac0b3d9cb71239dfda27da675c06e9090f5dd2ca55fc108cc124c874768b1ff88b7ff000ed70aa126d99741dc6b2ddb603ad2f3c64fb1e81445

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=10090&attr_list=SOURCE_ID&attr_list=TARGET_ID&api_key=9603140cd6217ac0b3d9cb71239dfda27da675c06e9090f5dd2ca55fc108cc124c874768b1ff88b7ff000ed70aa126d99741dc6b2ddb603ad2f3c64fb1e81445&source=BgeeDB_R_package&source_version=2.12.1)
   Submitting URL to Bgee webservice (can be long)
trying URL 'https://r.bgee.org/bgee14_1/?page=r_package&action=get_anat_entity_relations&display_type=tsv&species_list=10090&attr_list=SOURCE_ID&attr_list=TARGET_ID&api_key=9603140cd6217ac0b3d9cb71239dfda27da675c06e9090f5dd2ca55fc108cc124c874768b1ff88b7ff000ed70aa126d99741dc6b2ddb603ad2f3c64fb1e81445&source=BgeeDB_R_package&source_version=2.12.1'
downloaded 915 KB

   Got results from Bgee webservice. Files are written in "/home/biocbuild/bbs-3.10-bioc/meat/BgeeDB.Rcheck/tests/testthat/Mus_musculus_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=10090&attr_list=ID&attr_list=NAME&api_key=9603140cd6217ac0b3d9cb71239dfda27da675c06e9090f5dd2ca55fc108cc124c874768b1ff88b7ff000ed70aa126d99741dc6b2ddb603ad2f3c64fb1e81445&source=BgeeDB_R_package&source_version=2.12.1)
   Submitting URL to Bgee webservice (can be long)
trying URL 'https://r.bgee.org/bgee14_1/?page=r_package&action=get_anat_entities&display_type=tsv&species_list=10090&attr_list=ID&attr_list=NAME&api_key=9603140cd6217ac0b3d9cb71239dfda27da675c06e9090f5dd2ca55fc108cc124c874768b1ff88b7ff000ed70aa126d99741dc6b2ddb603ad2f3c64fb1e81445&source=BgeeDB_R_package&source_version=2.12.1'
downloaded 841 KB

   Got results from Bgee webservice. Files are written in "/home/biocbuild/bbs-3.10-bioc/meat/BgeeDB.Rcheck/tests/testthat/Mus_musculus_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=10090&attr_list=GENE_ID&attr_list=ANAT_ENTITY_ID&api_key=9603140cd6217ac0b3d9cb71239dfda27da675c06e9090f5dd2ca55fc108cc124c874768b1ff88b7ff000ed70aa126d99741dc6b2ddb603ad2f3c64fb1e81445&source=BgeeDB_R_package&source_version=2.12.1&data_type=RNA_SEQ&data_qual=SILVER&stage_id=UBERON:0000106)
   Submitting URL to Bgee webservice (can be long)
trying URL 'https://r.bgee.org/bgee14_1/?page=r_package&action=get_expression_calls&display_type=tsv&species_list=10090&attr_list=GENE_ID&attr_list=ANAT_ENTITY_ID&api_key=9603140cd6217ac0b3d9cb71239dfda27da675c06e9090f5dd2ca55fc108cc124c874768b1ff88b7ff000ed70aa126d99741dc6b2ddb603ad2f3c64fb1e81445&source=BgeeDB_R_package&source_version=2.12.1&data_type=RNA_SEQ&data_qual=SILVER&stage_id=UBERON:0000106'
downloaded 1.3 MB

   Got results from Bgee webservice. Files are written in "/home/biocbuild/bbs-3.10-bioc/meat/BgeeDB.Rcheck/tests/testthat/Mus_musculus_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 /home/biocbuild/bbs-3.10-bioc/meat/BgeeDB.Rcheck/tests/testthat. Data will not be redownloaded.

API key built: 9603140cd6217ac0b3d9cb71239dfda27da675c06e9090f5dd2ca55fc108cc124c874768b1ff88b7ff000ed70aa126d99741dc6b2ddb603ad2f3c64fb1e81445
trying URL 'ftp://ftp.bgee.org/bgee_v14_1/download/processed_expr_values/rna_seq/Mus_musculus/Mus_musculus_RNA-Seq_read_counts_TPM_FPKM.tar.gz'
Content type 'unknown' length 174792438 bytes (166.7 MB)
==================================================

Querying Bgee to get release information...

NOTE: the file describing Bgee species information for release 14_1 was found in the download directory /home/biocbuild/bbs-3.10-bioc/meat/BgeeDB.Rcheck/tests/testthat. Data will not be redownloaded.

API key built: 9603140cd6217ac0b3d9cb71239dfda27da675c06e9090f5dd2ca55fc108cc124c874768b1ff88b7ff000ed70aa126d99741dc6b2ddb603ad2f3c64fb1e81445

Querying Bgee to get release information...

NOTE: the file describing Bgee species information for release 14_1 was found in the download directory /home/biocbuild/bbs-3.10-bioc/meat/BgeeDB.Rcheck/tests/testthat. Data will not be redownloaded.

API key built: 9603140cd6217ac0b3d9cb71239dfda27da675c06e9090f5dd2ca55fc108cc124c874768b1ff88b7ff000ed70aa126d99741dc6b2ddb603ad2f3c64fb1e81445

NOTE: an organ relationships file was found in the download directory /home/biocbuild/bbs-3.10-bioc/meat/BgeeDB.Rcheck/tests/testthat/Mus_musculus_Bgee_14_1. Data will not be redownloaded.

NOTE: an organ names file was found in the download directory /home/biocbuild/bbs-3.10-bioc/meat/BgeeDB.Rcheck/tests/testthat/Mus_musculus_Bgee_14_1. Data will not be redownloaded.

NOTE: a gene to organs mapping file was found in the download directory /home/biocbuild/bbs-3.10-bioc/meat/BgeeDB.Rcheck/tests/testthat/Mus_musculus_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......................

WARNING: Some genes in your gene list have no expression data in Bgee, and will not be included in the analysis. 85 genes in background will be kept.

Building most specific Ontology terms...  (  2  Ontology terms found. )

Building DAG topology...................  (  13  Ontology terms and  14  relations. )

Annotating nodes (Can be long)..........  (  85  genes annotated to the Ontology terms. )
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 30 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
266.564  13.744 364.527 

name	user	system	elapsed
Bgee-class	0.240	0.012	4.421
formatData	3.148	0.228	7.537
geneList	13.824	0.252	41.421
getAnnotation	0.016	0.076	4.547
getData	224.540	12.668	241.969
listBgeeRelease	0.004	0.004	2.127
listBgeeSpecies	0.524	0.032	8.522
loadTopAnatData	8.540	0.392	169.127
makeTable	7.444	0.084	9.901
topAnat	5.772	0.040	8.688