| Back to Build/check report for BioC 3.17: simplified long |
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This page was generated on 2023-03-27 05:50:33 -0000 (Mon, 27 Mar 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-03-12 r83975) -- "Unsuffered Consequences" | 6083 |
| 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 | ||||
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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 622/2195 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ensembldb 2.23.2 (landing page) Johannes Rainer
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | OK | |||||||||
| Package: ensembldb |
| Version: 2.23.2 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:ensembldb.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings ensembldb_2.23.2.tar.gz |
| StartedAt: 2023-03-25 01:49:21 -0000 (Sat, 25 Mar 2023) |
| EndedAt: 2023-03-25 02:02:34 -0000 (Sat, 25 Mar 2023) |
| EllapsedTime: 793.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ensembldb.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:ensembldb.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings ensembldb_2.23.2.tar.gz
###
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##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/ensembldb.Rcheck’
* using R Under development (unstable) (2023-03-12 r83975)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* using session charset: UTF-8
* checking for file ‘ensembldb/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ensembldb’ version ‘2.23.2’
* 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 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
Filter-classes 2.538 1.832 9.265
EnsDb-AnnotationDbi 3.616 0.501 5.466
EnsDb-exonsBy 2.490 1.569 9.879
* 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 ...
‘MySQL-backend.Rmd’ using ‘UTF-8’... OK
‘coordinate-mapping-use-cases.Rmd’ using ‘UTF-8’... OK
‘coordinate-mapping.Rmd’ using ‘UTF-8’... OK
‘ensembldb.Rmd’ using ‘UTF-8’... OK
‘proteins.Rmd’ using ‘UTF-8’... OK
NONE
* 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-3.17-bioc/R/bin/R CMD INSTALL ensembldb ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-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 Under development (unstable) (2023-03-12 r83975) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (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/Rtmpgn3AV8/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 : Sat Mar 25 01:56:53 2023 != Sat Mar 25 01:56:40 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 80 | SKIP 3 | PASS 1481 ]
══ Skipped tests ═══════════════════════════════════════════════════════════════
• empty test (3)
[ FAIL 0 | WARN 80 | SKIP 3 | PASS 1481 ]
Warning message:
call dbDisconnect() when finished working with a connection
>
> proc.time()
user system elapsed
164.717 22.580 273.922
ensembldb.Rcheck/ensembldb-Ex.timings
| name | user | system | elapsed | |
| EnsDb-AnnotationDbi | 3.616 | 0.501 | 5.466 | |
| EnsDb-class | 0.891 | 0.171 | 1.123 | |
| EnsDb-exonsBy | 2.490 | 1.569 | 9.879 | |
| EnsDb-lengths | 1.136 | 0.166 | 1.309 | |
| EnsDb-seqlevels | 0.056 | 0.017 | 0.076 | |
| EnsDb-sequences | 0.016 | 0.000 | 0.016 | |
| EnsDb-utils | 0.318 | 0.007 | 0.357 | |
| EnsDb | 1.171 | 0.138 | 1.328 | |
| Filter-classes | 2.538 | 1.832 | 9.265 | |
| ProteinFunctionality | 0.059 | 0.035 | 0.100 | |
| cdsToTranscript | 2.001 | 0.047 | 2.057 | |
| convertFilter | 0.031 | 0.001 | 0.031 | |
| genomeToProtein | 2.364 | 0.159 | 2.525 | |
| genomeToTranscript | 1.915 | 0.169 | 2.581 | |
| global-filters | 0.121 | 0.004 | 0.142 | |
| hasProteinData-EnsDb-method | 0.014 | 0.000 | 0.014 | |
| listEnsDbs | 0 | 0 | 0 | |
| makeEnsemblDbPackage | 0.765 | 0.019 | 0.790 | |
| proteinToGenome | 2.557 | 0.172 | 2.734 | |
| proteinToTranscript | 1.020 | 0.108 | 1.129 | |
| transcriptToCds | 0.705 | 0.019 | 0.725 | |
| transcriptToGenome | 1.243 | 0.016 | 1.261 | |
| transcriptToProtein | 2.241 | 0.099 | 2.340 | |
| useMySQL-EnsDb-method | 0.014 | 0.000 | 0.014 | |