Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-12-23 12:03 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
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 651/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
ensembldb 2.30.0 (landing page) Johannes Rainer
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | |||||||||
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. |
Package: ensembldb |
Version: 2.30.0 |
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:ensembldb.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings ensembldb_2.30.0.tar.gz |
StartedAt: 2024-12-19 23:17:44 -0500 (Thu, 19 Dec 2024) |
EndedAt: 2024-12-19 23:38:01 -0500 (Thu, 19 Dec 2024) |
EllapsedTime: 1216.9 seconds |
RetCode: 0 |
Status: OK |
CheckDir: ensembldb.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:ensembldb.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings ensembldb_2.30.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/ensembldb.Rcheck’ * using R version 4.4.2 (2024-10-31) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 * running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * checking for file ‘ensembldb/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘ensembldb’ version ‘2.30.0’ * 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 loading without being on the library search path ... 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 transcriptToGenome 34.783 6.842 183.029 cdsToTranscript 16.355 4.547 21.054 transcriptToCds 12.209 4.391 16.614 genomeToTranscript 10.256 3.358 55.227 * 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 re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: OK
ensembldb.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL ensembldb ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-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)
ensembldb.Rcheck/tests/testthat.Rout
R version 4.4.2 (2024-10-31) -- "Pile of Leaves" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu 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, saveRDS, 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 /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpILbpeg/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 : Thu Dec 19 23:31:23 2024 != Thu Dec 19 23:31:17 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 265.764 43.660 344.044
ensembldb.Rcheck/ensembldb-Ex.timings
name | user | system | elapsed | |
EnsDb-AnnotationDbi | 1.780 | 0.229 | 2.504 | |
EnsDb-class | 0.668 | 0.043 | 0.711 | |
EnsDb-exonsBy | 1.715 | 0.318 | 2.671 | |
EnsDb-lengths | 0.809 | 0.076 | 0.884 | |
EnsDb-seqlevels | 0.043 | 0.003 | 0.046 | |
EnsDb-sequences | 0.009 | 0.000 | 0.008 | |
EnsDb-utils | 0.218 | 0.004 | 0.222 | |
EnsDb | 0.804 | 0.052 | 0.857 | |
Filter-classes | 1.593 | 0.868 | 3.565 | |
ProteinFunctionality | 0.053 | 0.010 | 0.062 | |
cdsToTranscript | 16.355 | 4.547 | 21.054 | |
convertFilter | 0.019 | 0.000 | 0.019 | |
genomeToProtein | 3.199 | 0.210 | 3.409 | |
genomeToTranscript | 10.256 | 3.358 | 55.227 | |
global-filters | 0.136 | 0.006 | 0.231 | |
hasProteinData-EnsDb-method | 0.012 | 0.000 | 0.012 | |
listEnsDbs | 0 | 0 | 0 | |
makeEnsemblDbPackage | 0.650 | 0.038 | 1.006 | |
proteinToGenome | 3.922 | 0.453 | 4.385 | |
proteinToTranscript | 2.001 | 0.339 | 2.341 | |
transcriptToCds | 12.209 | 4.391 | 16.614 | |
transcriptToGenome | 34.783 | 6.842 | 183.029 | |
transcriptToProtein | 2.725 | 0.400 | 3.574 | |
useMySQL-EnsDb-method | 0.008 | 0.001 | 0.009 | |