##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ensembldb.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ensembldb_2.28.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/ensembldb.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ensembldb/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ensembldb’ version ‘2.28.0’
* 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 ‘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 code 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 whether startup messages can be suppressed ... 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
cdsToTranscript     26.626 10.185  37.842
transcriptToGenome  22.939  9.382  88.275
transcriptToCds     22.033  9.713  32.335
genomeToTranscript  19.744 10.208  59.987
genomeToProtein      5.313  0.318   5.668
proteinToGenome      5.075  0.500   5.621
transcriptToProtein  4.532  0.248   5.069
Filter-classes       2.965  1.753   5.583
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: OK

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’
* installing *source* package ‘ensembldb’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Creating a generic function from function ‘.cds_for_id2’ in package ‘ensembldb’
** 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 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

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

Attaching package: 'BiocGenerics'

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, aperm, 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, table, tapply,
    union, unique, unsplit, 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:utils':

    findMatches

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

    I, expand.grid, unname

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/Rtmpby9F5K/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 : Mon Jun 17 19:52:17 2024  !=  Mon Jun 17 19:52:15 2024 
  -  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
[ FAIL 0 | WARN 75 | SKIP 3 | PASS 1628 ]

══ Skipped tests (3) ═══════════════════════════════════════════════════════════
• empty test (3): 'test_Methods.R:129:1', 'test_Methods.R:273:1',
  'test_seqLevelStyle.R:40:1'

[ FAIL 0 | WARN 75 | SKIP 3 | PASS 1628 ]
Warning message:
call dbDisconnect() when finished working with a connection 
> 
> proc.time()
   user  system elapsed 
414.259 103.171 536.081