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This page was generated on 2021-10-15 15:06:35 -0400 (Fri, 15 Oct 2021).
To the developers/maintainers of the ensembldb package: - Please 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 How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 576/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
ensembldb 2.16.4 (landing page) Johannes Rainer
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |||||||||
Package: ensembldb |
Version: 2.16.4 |
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_2.16.4.tar.gz |
StartedAt: 2021-10-14 18:44:12 -0400 (Thu, 14 Oct 2021) |
EndedAt: 2021-10-14 18:54:56 -0400 (Thu, 14 Oct 2021) |
EllapsedTime: 644.2 seconds |
RetCode: 0 |
Status: OK |
CheckDir: ensembldb.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### 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_2.16.4.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/ensembldb.Rcheck’ * using R version 4.1.1 (2021-08-10) * 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 ‘2.16.4’ * 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 3.665 2.460 8.584 EnsDb-AnnotationDbi 4.315 0.859 5.589 * 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
ensembldb.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL ensembldb ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/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)
ensembldb.Rcheck/tests/testthat.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things" Copyright (C) 2021 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.max, which.min Loading required package: GenomicRanges Loading required package: stats4 Loading required package: S4Vectors Attaching package: 'S4Vectors' 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/RtmpQ8QKwT/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 Oct 14 18:51:24 2021 != Thu Oct 14 18:51:15 2021 - 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 ══ Skipped tests ═══════════════════════════════════════════════════════════════ • empty test (3) [ FAIL 0 | WARN 82 | SKIP 3 | PASS 1458 ] There were 26 warnings (use warnings() to see them) > > proc.time() user system elapsed 208.262 25.808 292.734
ensembldb.Rcheck/ensembldb-Ex.timings
name | user | system | elapsed | |
EnsDb-AnnotationDbi | 4.315 | 0.859 | 5.589 | |
EnsDb-class | 0.915 | 0.098 | 1.012 | |
EnsDb-exonsBy | 3.317 | 0.858 | 4.966 | |
EnsDb-lengths | 1.681 | 0.126 | 1.808 | |
EnsDb-seqlevels | 0.058 | 0.015 | 0.073 | |
EnsDb-sequences | 0.020 | 0.002 | 0.021 | |
EnsDb-utils | 0.411 | 0.007 | 0.418 | |
EnsDb | 1.200 | 0.106 | 1.306 | |
Filter-classes | 3.665 | 2.460 | 8.584 | |
ProteinFunctionality | 0.102 | 0.022 | 0.123 | |
cdsToTranscript | 2.918 | 0.015 | 2.940 | |
convertFilter | 0.028 | 0.002 | 0.029 | |
genomeToProtein | 3.189 | 0.052 | 3.246 | |
genomeToTranscript | 2.528 | 0.088 | 2.618 | |
global-filters | 0.145 | 0.004 | 0.148 | |
hasProteinData-EnsDb-method | 0.016 | 0.000 | 0.017 | |
listEnsDbs | 0.000 | 0.000 | 0.001 | |
makeEnsemblDbPackage | 1.024 | 0.052 | 1.079 | |
proteinToGenome | 4.147 | 0.076 | 4.225 | |
proteinToTranscript | 1.559 | 0.061 | 1.620 | |
transcriptToCds | 0.800 | 0.001 | 0.802 | |
transcriptToGenome | 1.729 | 0.016 | 1.745 | |
transcriptToProtein | 3.397 | 0.061 | 3.460 | |
useMySQL-EnsDb-method | 0.013 | 0.001 | 0.014 | |