Package: ensembldb

Version: 2.10.2

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_2.10.2.tar.gz

StartedAt: 2020-04-15 02:06:24 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 02:16:25 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 600.7 seconds

RetCode: 0

Status:  OK

CheckDir: ensembldb.Rcheck

Warnings: 0

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### Running command:
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###   /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_2.10.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/ensembldb.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘2.10.2’
* 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 or elapsed time > 5s
                     user system elapsed
Filter-classes      3.862  2.461   9.423
EnsDb-AnnotationDbi 4.632  0.865   6.412
* 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

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL ensembldb
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/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)

R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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(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/Rtmp8cjAet/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 : Wed Apr 15 02:13:15 2020  !=  Wed Apr 15 02:13:07 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 19 warnings (use warnings() to see them)
> 
> proc.time()
   user  system elapsed 
202.666  33.736 283.046 

name	user	system	elapsed
EnsDb-AnnotationDbi	4.632	0.865	6.412
EnsDb-class	1.848	0.362	2.236
EnsDb-exonsBy	3.151	0.861	4.987
EnsDb-lengths	1.477	0.178	1.667
EnsDb-seqlevels	0.071	0.011	0.082
EnsDb-sequences	0.015	0.001	0.018
EnsDb-utils	0.284	0.008	0.294
EnsDb	2.105	0.294	2.418
Filter-classes	3.862	2.461	9.423
ProteinFunctionality	0.109	0.040	0.150
cdsToTranscript	2.215	0.035	2.266
convertFilter	0.024	0.001	0.025
genomeToProtein	2.669	0.043	2.732
genomeToTranscript	2.143	0.101	2.269
global-filters	0.153	0.005	0.157
hasProteinData-EnsDb-method	0.013	0.000	0.012
listEnsDbs	0	0	0
makeEnsemblDbPackage	0.977	0.039	1.034
proteinToGenome	2.951	0.114	3.162
proteinToTranscript	1.137	0.089	1.236
transcriptToCds	0.882	0.003	0.892
transcriptToGenome	1.519	0.018	1.542
transcriptToProtein	2.786	0.063	2.869
useMySQL-EnsDb-method	0.015	0.001	0.018