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CHECK report for BgeeDB on veracruz1

This page was generated on 2018-04-12 13:42:48 -0400 (Thu, 12 Apr 2018).

Package 108/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BgeeDB 2.5.0
Julien Wollbrett , Julien Roux , Andrea Komljenovic , Frederic Bastian
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/BgeeDB
Branch: RELEASE_3_6
Last Commit: 2869036
Last Changed Date: 2018-02-26 10:28:01 -0400 (Mon, 26 Feb 2018)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  ERROR  OK 
veracruz1 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: BgeeDB
Version: 2.5.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings BgeeDB_2.5.0.tar.gz
StartedAt: 2018-04-12 00:49:45 -0400 (Thu, 12 Apr 2018)
EndedAt: 2018-04-12 00:56:32 -0400 (Thu, 12 Apr 2018)
EllapsedTime: 407.3 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 --no-vignettes --timings BgeeDB_2.5.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/BgeeDB.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘2.5.0’
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
getData         71.630  5.109  89.393
loadTopAnatData  9.418  0.472  25.262
makeTable        7.815  0.286  10.693
topAnat          7.232  0.471   9.973
formatData       3.050  0.145   7.815
listBgeeSpecies  0.094  0.014   7.966
* 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

* installing *source* package ‘BgeeDB’ ...
** R
** data
** inst
** preparing 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

groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.
* DONE (BgeeDB)

Tests output

BgeeDB.Rcheck/tests/testthat.Rout


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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, cbind, colMeans, colSums, colnames, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
    pmin, pmin.int, rank, rbind, rowMeans, rowSums, 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

> 
> Sys.setenv("R_TESTS" = "")
> test_check("BgeeDB")

Querying Bgee to get release information...

Building URL to query species in Bgee release 14_0...

Submitting URL to Bgee webservice... (http://bgee.org/?page=r_package&action=get_all_species&display_type=tsv&source=BgeeDB_R_package&source_version=2.5.0)
trying URL 'http://bgee.org/?page=r_package&action=get_all_species&display_type=tsv&source=BgeeDB_R_package&source_version=2.5.0'
downloaded 1164 bytes


Query to Bgee webservice successful!

API key built: 5a115064fe827219c50b020e865b491aa711d83ee64f2e7821cc827095b2bcf76b932c6cc8fe7c13ffba3e7d3ed40d4112f855127b4ea21cd8614a5dd82936ac

Downloading expression data for the experiment GSE43721 ...
trying URL 'ftp://ftp.bgee.org/bgee_v14_beta/download/processed_expr_values/rna_seq/Mus_musculus/Mus_musculus_RNA-Seq_read_counts_TPM_FPKM_GSE43721.tsv.zip'
Content type 'unknown' length 1608495 bytes (1.5 MB)
==================================================

Saved expression data file in /Users/biocbuild/bbs-3.6-bioc/meat/BgeeDB.Rcheck/tests/testthat/Mus_musculus_Bgee_14_0 folder. Now unzip /Users/biocbuild/bbs-3.6-bioc/meat/BgeeDB.Rcheck/tests/testthat/Mus_musculus_Bgee_14_0/Mus_musculus_RNA-Seq_read_counts_TPM_FPKM_GSE43721.tsv.zip file...

Saving all data in .rds file...

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_0 was found in the download directory /Users/biocbuild/bbs-3.6-bioc/meat/BgeeDB.Rcheck/tests/testthat. Data will not be redownloaded.

API key built: 5a115064fe827219c50b020e865b491aa711d83ee64f2e7821cc827095b2bcf76b932c6cc8fe7c13ffba3e7d3ed40d4112f855127b4ea21cd8614a5dd82936ac

Downloading annotation files...
trying URL 'ftp://ftp.bgee.org/bgee_v14_beta/download/processed_expr_values/rna_seq/Mus_musculus/Mus_musculus_RNA-Seq_experiments_libraries.zip'
Content type 'unknown' length 11188 bytes (10 KB)
==================================================

Saved annotation files in /Users/biocbuild/bbs-3.6-bioc/meat/BgeeDB.Rcheck/tests/testthat/Mus_musculus_Bgee_14_0 folder.

Querying Bgee to get release information...

Building URL to query species in Bgee release 14...

Submitting URL to Bgee webservice... (http://bgee.org/?page=r_package&action=get_all_species&display_type=tsv&source=BgeeDB_R_package&source_version=2.5.0)
trying URL 'http://bgee.org/?page=r_package&action=get_all_species&display_type=tsv&source=BgeeDB_R_package&source_version=2.5.0'
downloaded 1164 bytes


Query to Bgee webservice successful!

Querying Bgee to get release information...

NOTE: the file describing Bgee species information for release 14_0 was found in the download directory /Users/biocbuild/bbs-3.6-bioc/meat/BgeeDB.Rcheck/tests/testthat. Data will not be redownloaded.

API key built: 5a115064fe827219c50b020e865b491aa711d83ee64f2e7821cc827095b2bcf76b932c6cc8fe7c13ffba3e7d3ed40d4112f855127b4ea21cd8614a5dd82936ac

Building URLs to retrieve organ relationships from Bgee.........
   URL successfully built (http://bgee.org/?page=r_package&action=get_anat_entity_relations&display_type=tsv&species_list=10090&attr_list=SOURCE_ID&attr_list=TARGET_ID&api_key=5a115064fe827219c50b020e865b491aa711d83ee64f2e7821cc827095b2bcf76b932c6cc8fe7c13ffba3e7d3ed40d4112f855127b4ea21cd8614a5dd82936ac&source=BgeeDB_R_package&source_version=2.5.0)
   Submitting URL to Bgee webservice (can be long)
trying URL 'http://bgee.org/?page=r_package&action=get_anat_entity_relations&display_type=tsv&species_list=10090&attr_list=SOURCE_ID&attr_list=TARGET_ID&api_key=5a115064fe827219c50b020e865b491aa711d83ee64f2e7821cc827095b2bcf76b932c6cc8fe7c13ffba3e7d3ed40d4112f855127b4ea21cd8614a5dd82936ac&source=BgeeDB_R_package&source_version=2.5.0'
downloaded 915 KB

   Got results from Bgee webservice. Files are written in "/Users/biocbuild/bbs-3.6-bioc/meat/BgeeDB.Rcheck/tests/testthat/Mus_musculus_Bgee_14_0"

Building URLs to retrieve organ names from Bgee.................
   URL successfully built (http://bgee.org/?page=r_package&action=get_anat_entities&display_type=tsv&species_list=10090&attr_list=ID&attr_list=NAME&api_key=5a115064fe827219c50b020e865b491aa711d83ee64f2e7821cc827095b2bcf76b932c6cc8fe7c13ffba3e7d3ed40d4112f855127b4ea21cd8614a5dd82936ac&source=BgeeDB_R_package&source_version=2.5.0)
   Submitting URL to Bgee webservice (can be long)
trying URL 'http://bgee.org/?page=r_package&action=get_anat_entities&display_type=tsv&species_list=10090&attr_list=ID&attr_list=NAME&api_key=5a115064fe827219c50b020e865b491aa711d83ee64f2e7821cc827095b2bcf76b932c6cc8fe7c13ffba3e7d3ed40d4112f855127b4ea21cd8614a5dd82936ac&source=BgeeDB_R_package&source_version=2.5.0'
downloaded 841 KB

   Got results from Bgee webservice. Files are written in "/Users/biocbuild/bbs-3.6-bioc/meat/BgeeDB.Rcheck/tests/testthat/Mus_musculus_Bgee_14_0"

Building URLs to retrieve mapping of gene to organs from Bgee...
   URL successfully built (http://bgee.org/?page=r_package&action=get_expression_calls&display_type=tsv&species_list=10090&attr_list=GENE_ID&attr_list=ANAT_ENTITY_ID&api_key=5a115064fe827219c50b020e865b491aa711d83ee64f2e7821cc827095b2bcf76b932c6cc8fe7c13ffba3e7d3ed40d4112f855127b4ea21cd8614a5dd82936ac&source=BgeeDB_R_package&source_version=2.5.0&data_type=RNA_SEQ&data_qual=SILVER&stage_id=UBERON:0000106)
   Submitting URL to Bgee webservice (can be long)
trying URL 'http://bgee.org/?page=r_package&action=get_expression_calls&display_type=tsv&species_list=10090&attr_list=GENE_ID&attr_list=ANAT_ENTITY_ID&api_key=5a115064fe827219c50b020e865b491aa711d83ee64f2e7821cc827095b2bcf76b932c6cc8fe7c13ffba3e7d3ed40d4112f855127b4ea21cd8614a5dd82936ac&source=BgeeDB_R_package&source_version=2.5.0&data_type=RNA_SEQ&data_qual=SILVER&stage_id=UBERON:0000106'
downloaded 681 KB

   Got results from Bgee webservice. Files are written in "/Users/biocbuild/bbs-3.6-bioc/meat/BgeeDB.Rcheck/tests/testthat/Mus_musculus_Bgee_14_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 14_0 was found in the download directory /Users/biocbuild/bbs-3.6-bioc/meat/BgeeDB.Rcheck/tests/testthat. Data will not be redownloaded.

API key built: 5a115064fe827219c50b020e865b491aa711d83ee64f2e7821cc827095b2bcf76b932c6cc8fe7c13ffba3e7d3ed40d4112f855127b4ea21cd8614a5dd82936ac

The experiment is not defined. Hence taking all rna_seq experiments available for Mus_musculus.

Downloading expression data...
trying URL 'ftp://ftp.bgee.org/bgee_v14_beta/download/processed_expr_values/rna_seq/Mus_musculus/Mus_musculus_RNA-Seq_read_counts_TPM_FPKM.zip'
Content type 'unknown' length 65850927 bytes (62.8 MB)
==================================================

Saved expression data file in /Users/biocbuild/bbs-3.6-bioc/meat/BgeeDB.Rcheck/tests/testthat/Mus_musculus_Bgee_14_0 folder. Now unzip file...

Read 15.1% of 1718244 rows
Read 51.8% of 1718244 rows
Read 88.5% of 1718244 rows
Read 1718244 rows and 16 (of 16) columns from 0.284 GB file in 00:00:05

Read 96.1% of 811393 rows
Read 811393 rows and 16 (of 16) columns from 0.141 GB file in 00:00:03

Read 74.1% of 1240954 rows
Read 1240954 rows and 16 (of 16) columns from 0.213 GB file in 00:00:03

Saving all data in .rds file...

Querying Bgee to get release information...

NOTE: the file describing Bgee species information for release 14_0 was found in the download directory /Users/biocbuild/bbs-3.6-bioc/meat/BgeeDB.Rcheck/tests/testthat. Data will not be redownloaded.

API key built: 5a115064fe827219c50b020e865b491aa711d83ee64f2e7821cc827095b2bcf76b932c6cc8fe7c13ffba3e7d3ed40d4112f855127b4ea21cd8614a5dd82936ac

NOTE: expression data file in .rds format was found in the download directory /Users/biocbuild/bbs-3.6-bioc/meat/BgeeDB.Rcheck/tests/testthat/Mus_musculus_Bgee_14_0 for GSE43721. Data will not be redownloaded.

Querying Bgee to get release information...

NOTE: the file describing Bgee species information for release 14_0 was found in the download directory /Users/biocbuild/bbs-3.6-bioc/meat/BgeeDB.Rcheck/tests/testthat. Data will not be redownloaded.

API key built: 5a115064fe827219c50b020e865b491aa711d83ee64f2e7821cc827095b2bcf76b932c6cc8fe7c13ffba3e7d3ed40d4112f855127b4ea21cd8614a5dd82936ac

NOTE: an organ relationships file was found in the download directory /Users/biocbuild/bbs-3.6-bioc/meat/BgeeDB.Rcheck/tests/testthat/Mus_musculus_Bgee_14_0. Data will not be redownloaded.

NOTE: an organ names file was found in the download directory /Users/biocbuild/bbs-3.6-bioc/meat/BgeeDB.Rcheck/tests/testthat/Mus_musculus_Bgee_14_0. Data will not be redownloaded.

NOTE: a gene to organs mapping file was found in the download directory /Users/biocbuild/bbs-3.6-bioc/meat/BgeeDB.Rcheck/tests/testthat/Mus_musculus_Bgee_14_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. 78 genes in background will be kept.

Building most specific Ontology terms...  (  1  Ontology terms found. )

Building DAG topology...................  (  11  Ontology terms and  12  relations. )

Annotating nodes (Can be long)..........  (  78  genes annotated to the Ontology terms. )
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 20 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 79.801   5.853 122.219

Example timings

BgeeDB.Rcheck/BgeeDB-Ex.timings

nameusersystemelapsed
Bgee-class0.1740.0114.967
formatData3.0500.1457.815
getAnnotation0.0200.0073.428
getData71.630 5.10989.393
listBgeeRelease0.0070.0031.437
listBgeeSpecies0.0940.0147.966
loadTopAnatData 9.418 0.47225.262
makeTable 7.815 0.28610.693
topAnat7.2320.4719.973