Back to Multiple platform build/check report for BioC 3.15 |
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This page was generated on 2022-03-18 11:07:27 -0400 (Fri, 18 Mar 2022).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" | 4334 |
riesling1 | Windows Server 2019 Standard | x64 | R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" | 4097 |
palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" | 4083 |
merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" | 4134 |
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? 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 588/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
ensembldb 2.19.9 (landing page) Johannes Rainer
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK | |||||||||
riesling1 | Windows Server 2019 Standard / x64 | OK | OK | OK | OK | |||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |||||||||
Package: ensembldb |
Version: 2.19.9 |
Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ensembldb.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings ensembldb_2.19.9.tar.gz |
StartedAt: 2022-03-17 19:01:48 -0400 (Thu, 17 Mar 2022) |
EndedAt: 2022-03-17 19:09:32 -0400 (Thu, 17 Mar 2022) |
EllapsedTime: 464.8 seconds |
RetCode: 0 |
Status: OK |
CheckDir: ensembldb.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ensembldb.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings ensembldb_2.19.9.tar.gz ### ############################################################################## ############################################################################## * using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/ensembldb.Rcheck' * using R Under development (unstable) (2021-11-21 r81221) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'ensembldb/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'ensembldb' version '2.19.9' * 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 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 1.56 2.73 6.34 * 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: ### ### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL ensembldb ### ############################################################################## ############################################################################## * installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library' * installing *source* package 'ensembldb' ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'ensembldb' finding HTML links ... done Deprecated html EnsDb-AnnotationDbi html EnsDb-class html EnsDb-exonsBy html finding level-2 HTML links ... done EnsDb-lengths html EnsDb-seqlevels html EnsDb-sequences html EnsDb-utils html EnsDb html Filter-classes html ProteinFunctionality html cdsToTranscript html convertFilter html genomeToProtein html genomeToTranscript html global-filters html hasProteinData-EnsDb-method html listEnsDbs html makeEnsemblDbPackage html proteinToGenome html proteinToTranscript html runEnsDbApp html transcriptToCds html transcriptToGenome html transcriptToProtein html useMySQL-EnsDb-method html ** 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) Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") : DESCRIPTION file of package 'TitanCNA' is missing or broken done
ensembldb.Rcheck/tests/testthat.Rout
R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" Copyright (C) 2021 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 (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, 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 Attaching package: 'IRanges' The following object is masked from 'package:grDevices': windows 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 D:\biocbuild\bbs-3.15-bioc\tmpdir\Rtmp2J3XKg/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 Mar 17 19:06:47 2022 != Thu Mar 17 19:06:38 2022 - 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 1479 ] == Skipped tests =============================================================== * empty test (3) [ FAIL 0 | WARN 83 | SKIP 3 | PASS 1479 ] There were 26 warnings (use warnings() to see them) > > proc.time() user system elapsed 116.73 58.45 228.82
ensembldb.Rcheck/ensembldb-Ex.timings
name | user | system | elapsed | |
EnsDb-AnnotationDbi | 1.53 | 0.75 | 2.28 | |
EnsDb-class | 0.61 | 0.16 | 0.76 | |
EnsDb-exonsBy | 1.35 | 0.97 | 2.61 | |
EnsDb-lengths | 1.37 | 0.20 | 1.58 | |
EnsDb-seqlevels | 0.05 | 0.02 | 0.06 | |
EnsDb-sequences | 0 | 0 | 0 | |
EnsDb-utils | 0.19 | 0.00 | 0.19 | |
EnsDb | 0.48 | 0.17 | 0.66 | |
Filter-classes | 1.56 | 2.73 | 6.34 | |
ProteinFunctionality | 0.05 | 0.02 | 0.06 | |
cdsToTranscript | 0.97 | 0.02 | 0.99 | |
convertFilter | 0.01 | 0.00 | 0.01 | |
genomeToProtein | 1.24 | 0.04 | 1.28 | |
genomeToTranscript | 0.94 | 0.17 | 1.11 | |
global-filters | 0.07 | 0.00 | 0.08 | |
hasProteinData-EnsDb-method | 0.00 | 0.02 | 0.02 | |
listEnsDbs | 0 | 0 | 0 | |
makeEnsemblDbPackage | 0.46 | 0.02 | 0.50 | |
proteinToGenome | 1.23 | 0.10 | 1.34 | |
proteinToTranscript | 0.56 | 0.13 | 0.69 | |
transcriptToCds | 0.38 | 0.00 | 0.37 | |
transcriptToGenome | 0.62 | 0.00 | 0.63 | |
transcriptToProtein | 1.21 | 0.06 | 1.26 | |
useMySQL-EnsDb-method | 0 | 0 | 0 | |