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This page was generated on 2024-11-26 11:44 -0500 (Tue, 26 Nov 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" 4748
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" 4459
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4350
kjohnson3macOS 13.6.5 Venturaarm64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4108
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 644/2272HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ensembldb 2.31.0  (landing page)
Johannes Rainer
Snapshot Date: 2024-11-25 13:40 -0500 (Mon, 25 Nov 2024)
git_url: https://git.bioconductor.org/packages/ensembldb
git_branch: devel
git_last_commit: 9c06161
git_last_commit_date: 2024-10-29 09:59:38 -0500 (Tue, 29 Oct 2024)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  NO, package depends on 'rtracklayer' which is only available as a source package that needs compilation
kjohnson3macOS 13.6.5 Ventura / arm64  OK    OK    OK    OK  NO, package depends on 'rtracklayer' which is only available as a source package that needs compilation


CHECK results for ensembldb on kjohnson3

To the developers/maintainers of the ensembldb package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ensembldb.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: ensembldb
Version: 2.31.0
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_2.31.0.tar.gz
StartedAt: 2024-11-25 21:52:13 -0500 (Mon, 25 Nov 2024)
EndedAt: 2024-11-25 22:01:21 -0500 (Mon, 25 Nov 2024)
EllapsedTime: 547.4 seconds
RetCode: 0
Status:   OK  
CheckDir: ensembldb.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### 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_2.31.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/ensembldb.Rcheck’
* using R Under development (unstable) (2024-11-20 r87352)
* 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 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ensembldb/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ensembldb’ version ‘2.31.0’
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  EnsDb-exonsBy.Rd: supportedFilters, GRangesFilter
  EnsDb-sequences.Rd: TwoBitFile-class
  Filter-classes.Rd: AnnotationFilter, supportedFilters, GeneIdFilter
  ProteinFunctionality.Rd: supportedFilters
  proteinToTranscript.Rd: fiveUTRsByTranscript
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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    6.769  2.054   8.963
transcriptToGenome 6.538  2.273  30.253
transcriptToCds    4.872  1.907   6.793
genomeToTranscript 4.831  1.723  13.626
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.21-bioc/meat/ensembldb.Rcheck/00check.log’
for details.


Installation output

ensembldb.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-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)

Tests output

ensembldb.Rcheck/tests/testthat.Rout


R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences"
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
Loading required package: generics

Attaching package: 'generics'

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

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


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, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, 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 /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpQY6bhX/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 Nov 25 21:59:00 2024  !=  Mon Nov 25 21:58:54 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 1632 ]

══ 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 1632 ]
Warning message:
call dbDisconnect() when finished working with a connection 
> 
> proc.time()
   user  system elapsed 
108.291  23.292 168.325 

Example timings

ensembldb.Rcheck/ensembldb-Ex.timings

nameusersystemelapsed
EnsDb-AnnotationDbi0.5710.1740.996
EnsDb-class0.2340.0550.290
EnsDb-exonsBy0.6240.2151.027
EnsDb-lengths0.2700.0500.319
EnsDb-seqlevels0.0150.0060.020
EnsDb-sequences0.0030.0000.004
EnsDb-utils0.0590.0040.063
EnsDb0.2930.0520.344
Filter-classes0.7540.6811.980
ProteinFunctionality0.0200.0050.025
cdsToTranscript6.7692.0548.963
convertFilter0.0060.0000.006
genomeToProtein0.8880.0640.952
genomeToTranscript 4.831 1.72313.626
global-filters0.0250.0020.026
hasProteinData-EnsDb-method0.0030.0000.003
listEnsDbs000
makeEnsemblDbPackage0.1810.0130.196
proteinToGenome1.0390.1091.155
proteinToTranscript0.6200.1160.745
transcriptToCds4.8721.9076.793
transcriptToGenome 6.538 2.27330.253
transcriptToProtein0.7110.0660.778
useMySQL-EnsDb-method0.0030.0000.004