Back to Multiple platform build/check report for BioC 3.16: simplified long |
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This page was generated on 2023-04-12 11:06:06 -0400 (Wed, 12 Apr 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4502 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" | 4282 |
lconway | macOS 12.5.1 Monterey | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4310 |
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 |
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? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 613/2183 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
ensembldb 2.22.0 (landing page) Johannes Rainer
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.5.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
Package: ensembldb |
Version: 2.22.0 |
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_2.22.0.tar.gz |
StartedAt: 2023-04-10 20:03:41 -0400 (Mon, 10 Apr 2023) |
EndedAt: 2023-04-10 20:11:25 -0400 (Mon, 10 Apr 2023) |
EllapsedTime: 464.0 seconds |
RetCode: 0 |
Status: OK |
CheckDir: ensembldb.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### 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_2.22.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.16-bioc/meat/ensembldb.Rcheck’ * using R version 4.2.3 (2023-03-15) * 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 ‘2.22.0’ * 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 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 2.787 2.288 7.515 * 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/Resources/bin/R CMD INSTALL ensembldb ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/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 4.2.3 (2023-03-15) -- "Shortstop Beagle" Copyright (C) 2023 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 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, 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/RtmpqZjTbL/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 Apr 10 20:09:08 2023 != Mon Apr 10 20:08:59 2023 - 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 83 | SKIP 3 | PASS 1483 ] ══ Skipped tests ═══════════════════════════════════════════════════════════════ • empty test (3) [ FAIL 0 | WARN 83 | SKIP 3 | PASS 1483 ] There were 26 warnings (use warnings() to see them) > > proc.time() user system elapsed 128.009 22.349 212.011
ensembldb.Rcheck/ensembldb-Ex.timings
name | user | system | elapsed | |
EnsDb-AnnotationDbi | 3.114 | 0.668 | 4.265 | |
EnsDb-class | 0.729 | 0.088 | 0.825 | |
EnsDb-exonsBy | 2.055 | 0.728 | 3.729 | |
EnsDb-lengths | 0.993 | 0.102 | 1.110 | |
EnsDb-seqlevels | 0.052 | 0.016 | 0.069 | |
EnsDb-sequences | 0.018 | 0.001 | 0.020 | |
EnsDb-utils | 0.217 | 0.004 | 0.222 | |
EnsDb | 0.811 | 0.091 | 0.912 | |
Filter-classes | 2.787 | 2.288 | 7.515 | |
ProteinFunctionality | 0.070 | 0.019 | 0.091 | |
cdsToTranscript | 1.466 | 0.011 | 1.486 | |
convertFilter | 0.029 | 0.002 | 0.031 | |
genomeToProtein | 1.614 | 0.039 | 1.659 | |
genomeToTranscript | 1.324 | 0.081 | 1.417 | |
global-filters | 0.112 | 0.007 | 0.118 | |
hasProteinData-EnsDb-method | 0.014 | 0.001 | 0.014 | |
listEnsDbs | 0 | 0 | 0 | |
makeEnsemblDbPackage | 0.570 | 0.042 | 0.622 | |
proteinToGenome | 1.765 | 0.058 | 1.830 | |
proteinToTranscript | 0.700 | 0.057 | 0.761 | |
transcriptToCds | 0.435 | 0.002 | 0.437 | |
transcriptToGenome | 0.779 | 0.011 | 0.792 | |
transcriptToProtein | 1.654 | 0.039 | 1.697 | |
useMySQL-EnsDb-method | 0.017 | 0.001 | 0.018 | |