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CHECK report for ensembldb on machv2

This page was generated on 2020-10-17 11:58:26 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE ensembldb PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 548/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ensembldb 2.12.1
Johannes Rainer
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/ensembldb
Branch: RELEASE_3_11
Last Commit: ee79696
Last Changed Date: 2020-05-06 16:12:22 -0400 (Wed, 06 May 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: ensembldb
Version: 2.12.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ensembldb.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ensembldb_2.12.1.tar.gz
StartedAt: 2020-10-17 00:53:15 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 01:05:22 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 727.5 seconds
RetCode: 0
Status:  OK 
CheckDir: ensembldb.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ensembldb.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ensembldb_2.12.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/ensembldb.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 ‘ensembldb/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ensembldb’ 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 ‘ensembldb’ 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                     user system elapsed
Filter-classes      3.446  2.548   8.510
EnsDb-AnnotationDbi 4.441  0.991   6.035
EnsDb-exonsBy       3.439  0.830   5.111
* 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

ensembldb.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘ensembldb’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (ensembldb)

Tests output

ensembldb.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(ensembldb)
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: GenomicRanges
Loading required package: stats4
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: GenomicFeatures
Loading required package: AnnotationDbi
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: AnnotationFilter

Attaching package: 'AnnotationFilter'

The following object is masked from 'package:testthat':

    not


Attaching package: 'ensembldb'

The following object is masked from 'package:stats':

    filter

> library(EnsDb.Hsapiens.v86)
> edb <- EnsDb.Hsapiens.v86
> 
> test_check("ensembldb")
Creating package in /tmp/RtmpQ7Pvz1/EnsDb.Hsapiens.v75 

Comparing chromosome data:
 Sequence names: (180) common, (0) only in x, (0) only in y.
 Sequence lengths: (180) identical, (0) different.
Done. Result: OK

Comparing gene data:
 gene IDs: (4045) common, (0) only in x, (0) only in y.
 Sequence names: (4045) identical, (0) different.
 Gene start coordinates: (4045) identical, (0) different.
 Gene end coordinates: (4045) identical, (0) different.
 Gene strand: (4045) identical, (0) different.
 Gene names: (132) identical, (3913) different.
 Entrezgene IDs: (4045) identical, (0) different.
 Gene biotypes: (4045) identical, (0) different.
Done. Result: WARN

Comparing transcript data:
 transcript IDs: (4045) common, (0) only in x, (0) only in y.
 Transcript start coordinates: (4045) identical, (0) different.
 Transcript end coordinates: (4045) identical, (0) different.
 Transcript biotypes: (4045) identical, (0) different.
 Common transcripts with defined CDS: (3996) common, (0) only in x, (0) only in y.
 CDS start coordinates: (3996) identical, (0) different.
 CDS end coordinates: (3996) identical, (0) different.
 Associated gene IDs: (4045) identical, (0) different.
Done. Result: OK

Comparing exon data:
 exon IDs: (4045) common, (0) only in x, (0) only in y.
 Exon start coordinates: (4045) identical, (0) different.
 Exon end coordinates: (4045) identical, (0) different.
 Exon index in transcript models: (4045) identical, (0) different.
Done. Result: OK

Comparing metadata:
 Ensembl versions match.
 Genome builds match.
 All differences: <name>: <value x> != <value y>
  -  Creation time : Sat Oct 17 01:01:59 2020  !=  Sat Oct 17 01:01:50 2020 
  -  source_file : Devosia_geojensis.ASM96941v1.32.gtf.gz  !=  Devosia_geojensis.ASM96941v1.32.gff3.gz 
Done. Result: NOTE

Comparing chromosome data:
 Sequence names: (180) common, (0) only in x, (0) only in y.
 Sequence lengths: (180) identical, (0) different.
Done. Result: OK

Comparing gene data:
 gene IDs: (4045) common, (0) only in x, (0) only in y.
 Sequence names: (4045) identical, (0) different.
 Gene start coordinates: (4045) identical, (0) different.
 Gene end coordinates: (4045) identical, (0) different.
 Gene strand: (4045) identical, (0) different.
 Gene names: (132) identical, (3913) different.
 Entrezgene IDs: (4045) identical, (0) different.
 Gene biotypes: (4045) identical, (0) different.
Done. Result: WARN

Comparing transcript data:
 transcript IDs: (4045) common, (0) only in x, (0) only in y.
 Transcript start coordinates: (4045) identical, (0) different.
 Transcript end coordinates: (4045) identical, (0) different.
 Transcript biotypes: (4045) identical, (0) different.
 Common transcripts with defined CDS: (3996) common, (0) only in x, (0) only in y.
 CDS start coordinates: (3996) identical, (0) different.
 CDS end coordinates: (3996) identical, (0) different.
 Associated gene IDs: (4045) identical, (0) different.
Done. Result: OK

Comparing exon data:
 exon IDs: (4045) common, (0) only in x, (0) only in y.
 Exon start coordinates: (4045) identical, (0) different.
 Exon end coordinates: (4045) identical, (0) different.
 Exon index in transcript models: (4045) identical, (0) different.
Done. Result: OK

Comparing protein data:
 protein IDs: (103725) common, (0) only in x, (0) only in y.
 Transcript IDs: (103725) identical, (0) different.
 Protein sequence: (103725) identical, (0) different.
Done. Result: OK
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 1449 | SKIPPED: 3 | WARNINGS: 82 | FAILED: 0 ]
There were 26 warnings (use warnings() to see them)
> 
> proc.time()
   user  system elapsed 
211.959  27.879 287.567 

Example timings

ensembldb.Rcheck/ensembldb-Ex.timings

nameusersystemelapsed
EnsDb-AnnotationDbi4.4410.9916.035
EnsDb-class1.8770.2172.099
EnsDb-exonsBy3.4390.8305.111
EnsDb-lengths1.6830.1771.863
EnsDb-seqlevels0.0940.0220.114
EnsDb-sequences0.0160.0010.018
EnsDb-utils0.4110.0070.417
EnsDb2.1830.2172.401
Filter-classes3.4462.5488.510
ProteinFunctionality0.1140.0250.139
cdsToTranscript2.4720.0792.555
convertFilter0.0240.0010.025
genomeToProtein2.7870.0552.850
genomeToTranscript2.3520.1082.465
global-filters0.1170.0040.120
hasProteinData-EnsDb-method0.0200.0010.021
listEnsDbs0.0010.0000.001
makeEnsemblDbPackage0.9610.0541.022
proteinToGenome3.3340.0853.423
proteinToTranscript1.4450.0931.541
transcriptToCds0.8470.0040.851
transcriptToGenome1.6690.0211.692
transcriptToProtein3.0440.0573.108
useMySQL-EnsDb-method0.0180.0010.020