Johannes Rainer
| Snapshot Date: 2024-05-11 09:00:03 -0400 (Sat, 11 May 2024) |
| git_url: https://git.bioconductor.org/packages/ensembldb |
| git_branch: devel |
| git_last_commit: f9c0e8c |
| git_last_commit_date: 2024-04-30 10:42:33 -0400 (Tue, 30 Apr 2024) |
| Back to Mac ARM64 build report for BioC 3.20 |
|
This page was generated on 2024-05-13 11:32:03 -0400 (Mon, 13 May 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4378 |
| 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 634/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ensembldb 2.29.0 (landing page) Johannes Rainer
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | | |||||||
|
To the developers/maintainers of the ensembldb package: - 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: 2.29.0 |
| 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_2.29.0.tar.gz |
| StartedAt: 2024-05-12 12:42:02 -0400 (Sun, 12 May 2024) |
| EndedAt: 2024-05-12 13:00:21 -0400 (Sun, 12 May 2024) |
| EllapsedTime: 1099.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ensembldb.Rcheck |
| Warnings: 0 |
##############################################################################
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### Running command:
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### /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_2.29.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc-mac-arm64/meat/ensembldb.Rcheck’
* using R version 4.4.0 Patched (2024-04-24 r86482)
* using platform: aarch64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ensembldb/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ensembldb’ version ‘2.29.0’
* 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 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 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
cdsToTranscript 27.200 9.993 37.878
transcriptToGenome 24.479 9.340 89.448
transcriptToCds 22.241 11.132 33.927
genomeToTranscript 19.715 9.767 57.275
genomeToProtein 5.277 0.292 5.596
proteinToGenome 5.018 0.494 5.571
Filter-classes 2.967 1.909 5.725
* 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 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/4.4-arm64/Resources/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 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20
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, 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 /tmp/RtmpH56ncH/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 : Sun May 12 12:52:34 2024 != Sun May 12 12:52:32 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 1628 ]
══ 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 1628 ]
Warning message:
call dbDisconnect() when finished working with a connection
>
> proc.time()
user system elapsed
414.441 103.501 535.781
ensembldb.Rcheck/ensembldb-Ex.timings
| name | user | system | elapsed | |
| EnsDb-AnnotationDbi | 3.454 | 0.696 | 4.512 | |
| EnsDb-class | 1.081 | 0.128 | 1.219 | |
| EnsDb-exonsBy | 2.442 | 0.619 | 3.362 | |
| EnsDb-lengths | 1.095 | 0.142 | 1.268 | |
| EnsDb-seqlevels | 0.065 | 0.020 | 0.084 | |
| EnsDb-sequences | 0.017 | 0.002 | 0.018 | |
| EnsDb-utils | 0.252 | 0.008 | 0.260 | |
| EnsDb | 1.609 | 0.115 | 1.734 | |
| Filter-classes | 2.967 | 1.909 | 5.725 | |
| ProteinFunctionality | 0.078 | 0.019 | 0.097 | |
| cdsToTranscript | 27.200 | 9.993 | 37.878 | |
| convertFilter | 0.025 | 0.002 | 0.027 | |
| genomeToProtein | 5.277 | 0.292 | 5.596 | |
| genomeToTranscript | 19.715 | 9.767 | 57.275 | |
| global-filters | 0.113 | 0.017 | 0.383 | |
| hasProteinData-EnsDb-method | 0.016 | 0.001 | 0.017 | |
| listEnsDbs | 0 | 0 | 0 | |
| makeEnsemblDbPackage | 0.673 | 0.053 | 0.731 | |
| proteinToGenome | 5.018 | 0.494 | 5.571 | |
| proteinToTranscript | 2.614 | 0.533 | 3.213 | |
| transcriptToCds | 22.241 | 11.132 | 33.927 | |
| transcriptToGenome | 24.479 | 9.340 | 89.448 | |
| transcriptToProtein | 2.949 | 0.245 | 3.526 | |
| useMySQL-EnsDb-method | 0.016 | 0.001 | 0.017 | |