Felix G.M. Ernst
| Snapshot Date: 2024-11-08 13:40 -0500 (Fri, 08 Nov 2024) |
| git_url: https://git.bioconductor.org/packages/EpiTxDb |
| git_branch: RELEASE_3_20 |
| git_last_commit: 421b805 |
| git_last_commit_date: 2024-10-29 10:44:25 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-11-09 21:30 -0500 (Sat, 09 Nov 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4505 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4506 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4538 |
| kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4486 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4493 |
| 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 666/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| EpiTxDb 1.18.0 (landing page) Felix G.M. Ernst
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | WARNINGS | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
|
To the developers/maintainers of the EpiTxDb package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/EpiTxDb.git to reflect on this report. See Troubleshooting Build Report for more information. - 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: EpiTxDb |
| Version: 1.18.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:EpiTxDb.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings EpiTxDb_1.18.0.tar.gz |
| StartedAt: 2024-11-09 01:51:26 -0500 (Sat, 09 Nov 2024) |
| EndedAt: 2024-11-09 01:56:53 -0500 (Sat, 09 Nov 2024) |
| EllapsedTime: 327.2 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: EpiTxDb.Rcheck |
| Warnings: 1 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:EpiTxDb.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings EpiTxDb_1.18.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/EpiTxDb.Rcheck’
* using R version 4.4.1 (2024-06-14)
* 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 13.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘EpiTxDb/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘EpiTxDb’ version ‘1.18.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
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 ‘EpiTxDb’ can be installed ... WARNING
Found the following significant warnings:
Warning: replacing previous import ‘GenomicFeatures::makeTxDbPackage’ by ‘txdbmaker::makeTxDbPackage’ when loading ‘EpiTxDb’
Warning: replacing previous import ‘GenomicFeatures::supportedUCSCFeatureDbTables’ by ‘txdbmaker::supportedUCSCFeatureDbTables’ when loading ‘EpiTxDb’
Warning: replacing previous import ‘GenomicFeatures::makeTxDbFromGFF’ by ‘txdbmaker::makeTxDbFromGFF’ when loading ‘EpiTxDb’
Warning: replacing previous import ‘GenomicFeatures::makeTxDbPackageFromBiomart’ by ‘txdbmaker::makeTxDbPackageFromBiomart’ when loading ‘EpiTxDb’
Warning: replacing previous import ‘GenomicFeatures::supportedMiRBaseBuildValues’ by ‘txdbmaker::supportedMiRBaseBuildValues’ when loading ‘EpiTxDb’
Warning: replacing previous import ‘GenomicFeatures::supportedUCSCFeatureDbTracks’ by ‘txdbmaker::supportedUCSCFeatureDbTracks’ when loading ‘EpiTxDb’
Warning: replacing previous import ‘GenomicFeatures::browseUCSCtrack’ by ‘txdbmaker::browseUCSCtrack’ when loading ‘EpiTxDb’
Warning: replacing previous import ‘GenomicFeatures::getChromInfoFromBiomart’ by ‘txdbmaker::getChromInfoFromBiomart’ when loading ‘EpiTxDb’
Warning: replacing previous import ‘GenomicFeatures::makeTxDbFromGRanges’ by ‘txdbmaker::makeTxDbFromGRanges’ when loading ‘EpiTxDb’
Warning: replacing previous import ‘GenomicFeatures::supportedUCSCtables’ by ‘txdbmaker::supportedUCSCtables’ when loading ‘EpiTxDb’
Warning: replacing previous import ‘GenomicFeatures::makeTxDbFromBiomart’ by ‘txdbmaker::makeTxDbFromBiomart’ when loading ‘EpiTxDb’
Warning: replacing previous import ‘GenomicFeatures::UCSCFeatureDbTableSchema’ by ‘txdbmaker::UCSCFeatureDbTableSchema’ when loading ‘EpiTxDb’
Warning: replacing previous import ‘GenomicFeatures::makeTxDbFromEnsembl’ by ‘txdbmaker::makeTxDbFromEnsembl’ when loading ‘EpiTxDb’
Warning: replacing previous import ‘GenomicFeatures::makeTxDb’ by ‘txdbmaker::makeTxDb’ when loading ‘EpiTxDb’
Warning: replacing previous import ‘GenomicFeatures::makeFDbPackageFromUCSC’ by ‘txdbmaker::makeFDbPackageFromUCSC’ when loading ‘EpiTxDb’
Warning: replacing previous import ‘GenomicFeatures::makeTxDbFromUCSC’ by ‘txdbmaker::makeTxDbFromUCSC’ when loading ‘EpiTxDb’
Warning: replacing previous import ‘GenomicFeatures::makeTxDbPackageFromUCSC’ by ‘txdbmaker::makeTxDbPackageFromUCSC’ when loading ‘EpiTxDb’
Warning: replacing previous import ‘GenomicFeatures::makePackageName’ by ‘txdbmaker::makePackageName’ when loading ‘EpiTxDb’
Warning: replacing previous import ‘GenomicFeatures::makeFeatureDbFromUCSC’ by ‘txdbmaker::makeFeatureDbFromUCSC’ when loading ‘EpiTxDb’
See ‘/Users/biocbuild/bbs-3.20-bioc/meat/EpiTxDb.Rcheck/00install.out’ for details.
* 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 dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
‘AnnotationDbi:::.getMetaValue’
‘AnnotationDbi:::.valid.metadata.table’
‘AnnotationDbi:::.valid.table.colnames’ ‘AnnotationDbi:::dbEasyQuery’
‘AnnotationDbi:::dbQuery’ ‘AnnotationDbi:::smartKeys’
‘BiocGenerics:::replaceSlots’
See the note in ?`:::` about the use of this operator.
* 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 ... NOTE
checkRd: (-1) makeEpiTxDb.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) makeEpiTxDb.Rd:21-23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) makeEpiTxDb.Rd:24-25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) makeEpiTxDb.Rd:26-27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) makeEpiTxDb.Rd:28-29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) makeEpiTxDb.Rd:30-31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) makeEpiTxDb.Rd:32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) makeEpiTxDb.Rd:33-34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) makeEpiTxDb.Rd:43-44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) makeEpiTxDb.Rd:45-46: Lost braces in \itemize; meant \describe ?
checkRd: (-1) makeEpiTxDb.Rd:47-49: Lost braces in \itemize; meant \describe ?
checkRd: (-1) makeEpiTxDb.Rd:50-51: Lost braces in \itemize; meant \describe ?
checkRd: (-1) makeEpiTxDb.Rd:52-53: Lost braces in \itemize; meant \describe ?
checkRd: (-1) makeEpiTxDb.Rd:54-55: Lost braces in \itemize; meant \describe ?
checkRd: (-1) makeEpiTxDb.Rd:62-63: Lost braces in \itemize; meant \describe ?
checkRd: (-1) makeEpiTxDb.Rd:64-66: Lost braces in \itemize; meant \describe ?
checkRd: (-1) makeEpiTxDb.Rd:67-69: Lost braces in \itemize; meant \describe ?
checkRd: (-1) makeEpiTxDb.Rd:70-71: Lost braces in \itemize; meant \describe ?
checkRd: (-1) makeEpiTxDb.Rd:72-73: Lost braces in \itemize; meant \describe ?
checkRd: (-1) makeEpiTxDb.Rd:74-75: Lost braces in \itemize; meant \describe ?
checkRd: (-1) makeEpiTxDb.Rd:82-83: Lost braces in \itemize; meant \describe ?
checkRd: (-1) makeEpiTxDb.Rd:84-85: Lost braces in \itemize; meant \describe ?
checkRd: (-1) makeEpiTxDb.Rd:86-88: Lost braces in \itemize; meant \describe ?
checkRd: (-1) makeEpiTxDb.Rd:94: Lost braces in \itemize; meant \describe ?
checkRd: (-1) makeEpiTxDb.Rd:95: Lost braces in \itemize; meant \describe ?
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* 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: 1 WARNING, 2 NOTEs
See
‘/Users/biocbuild/bbs-3.20-bioc/meat/EpiTxDb.Rcheck/00check.log’
for details.
EpiTxDb.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL EpiTxDb ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’ * installing *source* package ‘EpiTxDb’ ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading Warning: replacing previous import ‘GenomicFeatures::makeTxDbPackage’ by ‘txdbmaker::makeTxDbPackage’ when loading ‘EpiTxDb’ Warning: replacing previous import ‘GenomicFeatures::supportedUCSCFeatureDbTables’ by ‘txdbmaker::supportedUCSCFeatureDbTables’ when loading ‘EpiTxDb’ Warning: replacing previous import ‘GenomicFeatures::makeTxDbFromGFF’ by ‘txdbmaker::makeTxDbFromGFF’ when loading ‘EpiTxDb’ Warning: replacing previous import ‘GenomicFeatures::makeTxDbPackageFromBiomart’ by ‘txdbmaker::makeTxDbPackageFromBiomart’ when loading ‘EpiTxDb’ Warning: replacing previous import ‘GenomicFeatures::supportedMiRBaseBuildValues’ by ‘txdbmaker::supportedMiRBaseBuildValues’ when loading ‘EpiTxDb’ Warning: replacing previous import ‘GenomicFeatures::supportedUCSCFeatureDbTracks’ by ‘txdbmaker::supportedUCSCFeatureDbTracks’ when loading ‘EpiTxDb’ Warning: replacing previous import ‘GenomicFeatures::browseUCSCtrack’ by ‘txdbmaker::browseUCSCtrack’ when loading ‘EpiTxDb’ Warning: replacing previous import ‘GenomicFeatures::getChromInfoFromBiomart’ by ‘txdbmaker::getChromInfoFromBiomart’ when loading ‘EpiTxDb’ Warning: replacing previous import ‘GenomicFeatures::makeTxDbFromGRanges’ by ‘txdbmaker::makeTxDbFromGRanges’ when loading ‘EpiTxDb’ Warning: replacing previous import ‘GenomicFeatures::supportedUCSCtables’ by ‘txdbmaker::supportedUCSCtables’ when loading ‘EpiTxDb’ Warning: replacing previous import ‘GenomicFeatures::makeTxDbFromBiomart’ by ‘txdbmaker::makeTxDbFromBiomart’ when loading ‘EpiTxDb’ Warning: replacing previous import ‘GenomicFeatures::UCSCFeatureDbTableSchema’ by ‘txdbmaker::UCSCFeatureDbTableSchema’ when loading ‘EpiTxDb’ Warning: replacing previous import ‘GenomicFeatures::makeTxDbFromEnsembl’ by ‘txdbmaker::makeTxDbFromEnsembl’ when loading ‘EpiTxDb’ Warning: replacing previous import ‘GenomicFeatures::makeTxDb’ by ‘txdbmaker::makeTxDb’ when loading ‘EpiTxDb’ Warning: replacing previous import ‘GenomicFeatures::makeFDbPackageFromUCSC’ by ‘txdbmaker::makeFDbPackageFromUCSC’ when loading ‘EpiTxDb’ Warning: replacing previous import ‘GenomicFeatures::makeTxDbFromUCSC’ by ‘txdbmaker::makeTxDbFromUCSC’ when loading ‘EpiTxDb’ Warning: replacing previous import ‘GenomicFeatures::makeTxDbPackageFromUCSC’ by ‘txdbmaker::makeTxDbPackageFromUCSC’ when loading ‘EpiTxDb’ Warning: replacing previous import ‘GenomicFeatures::makePackageName’ by ‘txdbmaker::makePackageName’ when loading ‘EpiTxDb’ Warning: replacing previous import ‘GenomicFeatures::makeFeatureDbFromUCSC’ by ‘txdbmaker::makeFeatureDbFromUCSC’ when loading ‘EpiTxDb’ ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location Warning: replacing previous import ‘GenomicFeatures::makeTxDbPackage’ by ‘txdbmaker::makeTxDbPackage’ when loading ‘EpiTxDb’ Warning: replacing previous import ‘GenomicFeatures::supportedUCSCFeatureDbTables’ by ‘txdbmaker::supportedUCSCFeatureDbTables’ when loading ‘EpiTxDb’ Warning: replacing previous import ‘GenomicFeatures::makeTxDbFromGFF’ by ‘txdbmaker::makeTxDbFromGFF’ when loading ‘EpiTxDb’ Warning: replacing previous import ‘GenomicFeatures::makeTxDbPackageFromBiomart’ by ‘txdbmaker::makeTxDbPackageFromBiomart’ when loading ‘EpiTxDb’ Warning: replacing previous import ‘GenomicFeatures::supportedMiRBaseBuildValues’ by ‘txdbmaker::supportedMiRBaseBuildValues’ when loading ‘EpiTxDb’ Warning: replacing previous import ‘GenomicFeatures::supportedUCSCFeatureDbTracks’ by ‘txdbmaker::supportedUCSCFeatureDbTracks’ when loading ‘EpiTxDb’ Warning: replacing previous import ‘GenomicFeatures::browseUCSCtrack’ by ‘txdbmaker::browseUCSCtrack’ when loading ‘EpiTxDb’ Warning: replacing previous import ‘GenomicFeatures::getChromInfoFromBiomart’ by ‘txdbmaker::getChromInfoFromBiomart’ when loading ‘EpiTxDb’ Warning: replacing previous import ‘GenomicFeatures::makeTxDbFromGRanges’ by ‘txdbmaker::makeTxDbFromGRanges’ when loading ‘EpiTxDb’ Warning: replacing previous import ‘GenomicFeatures::supportedUCSCtables’ by ‘txdbmaker::supportedUCSCtables’ when loading ‘EpiTxDb’ Warning: replacing previous import ‘GenomicFeatures::makeTxDbFromBiomart’ by ‘txdbmaker::makeTxDbFromBiomart’ when loading ‘EpiTxDb’ Warning: replacing previous import ‘GenomicFeatures::UCSCFeatureDbTableSchema’ by ‘txdbmaker::UCSCFeatureDbTableSchema’ when loading ‘EpiTxDb’ Warning: replacing previous import ‘GenomicFeatures::makeTxDbFromEnsembl’ by ‘txdbmaker::makeTxDbFromEnsembl’ when loading ‘EpiTxDb’ Warning: replacing previous import ‘GenomicFeatures::makeTxDb’ by ‘txdbmaker::makeTxDb’ when loading ‘EpiTxDb’ Warning: replacing previous import ‘GenomicFeatures::makeFDbPackageFromUCSC’ by ‘txdbmaker::makeFDbPackageFromUCSC’ when loading ‘EpiTxDb’ Warning: replacing previous import ‘GenomicFeatures::makeTxDbFromUCSC’ by ‘txdbmaker::makeTxDbFromUCSC’ when loading ‘EpiTxDb’ Warning: replacing previous import ‘GenomicFeatures::makeTxDbPackageFromUCSC’ by ‘txdbmaker::makeTxDbPackageFromUCSC’ when loading ‘EpiTxDb’ Warning: replacing previous import ‘GenomicFeatures::makePackageName’ by ‘txdbmaker::makePackageName’ when loading ‘EpiTxDb’ Warning: replacing previous import ‘GenomicFeatures::makeFeatureDbFromUCSC’ by ‘txdbmaker::makeFeatureDbFromUCSC’ when loading ‘EpiTxDb’ ** testing if installed package can be loaded from final location Warning: replacing previous import ‘GenomicFeatures::makeTxDbPackage’ by ‘txdbmaker::makeTxDbPackage’ when loading ‘EpiTxDb’ Warning: replacing previous import ‘GenomicFeatures::supportedUCSCFeatureDbTables’ by ‘txdbmaker::supportedUCSCFeatureDbTables’ when loading ‘EpiTxDb’ Warning: replacing previous import ‘GenomicFeatures::makeTxDbFromGFF’ by ‘txdbmaker::makeTxDbFromGFF’ when loading ‘EpiTxDb’ Warning: replacing previous import ‘GenomicFeatures::makeTxDbPackageFromBiomart’ by ‘txdbmaker::makeTxDbPackageFromBiomart’ when loading ‘EpiTxDb’ Warning: replacing previous import ‘GenomicFeatures::supportedMiRBaseBuildValues’ by ‘txdbmaker::supportedMiRBaseBuildValues’ when loading ‘EpiTxDb’ Warning: replacing previous import ‘GenomicFeatures::supportedUCSCFeatureDbTracks’ by ‘txdbmaker::supportedUCSCFeatureDbTracks’ when loading ‘EpiTxDb’ Warning: replacing previous import ‘GenomicFeatures::browseUCSCtrack’ by ‘txdbmaker::browseUCSCtrack’ when loading ‘EpiTxDb’ Warning: replacing previous import ‘GenomicFeatures::getChromInfoFromBiomart’ by ‘txdbmaker::getChromInfoFromBiomart’ when loading ‘EpiTxDb’ Warning: replacing previous import ‘GenomicFeatures::makeTxDbFromGRanges’ by ‘txdbmaker::makeTxDbFromGRanges’ when loading ‘EpiTxDb’ Warning: replacing previous import ‘GenomicFeatures::supportedUCSCtables’ by ‘txdbmaker::supportedUCSCtables’ when loading ‘EpiTxDb’ Warning: replacing previous import ‘GenomicFeatures::makeTxDbFromBiomart’ by ‘txdbmaker::makeTxDbFromBiomart’ when loading ‘EpiTxDb’ Warning: replacing previous import ‘GenomicFeatures::UCSCFeatureDbTableSchema’ by ‘txdbmaker::UCSCFeatureDbTableSchema’ when loading ‘EpiTxDb’ Warning: replacing previous import ‘GenomicFeatures::makeTxDbFromEnsembl’ by ‘txdbmaker::makeTxDbFromEnsembl’ when loading ‘EpiTxDb’ Warning: replacing previous import ‘GenomicFeatures::makeTxDb’ by ‘txdbmaker::makeTxDb’ when loading ‘EpiTxDb’ Warning: replacing previous import ‘GenomicFeatures::makeFDbPackageFromUCSC’ by ‘txdbmaker::makeFDbPackageFromUCSC’ when loading ‘EpiTxDb’ Warning: replacing previous import ‘GenomicFeatures::makeTxDbFromUCSC’ by ‘txdbmaker::makeTxDbFromUCSC’ when loading ‘EpiTxDb’ Warning: replacing previous import ‘GenomicFeatures::makeTxDbPackageFromUCSC’ by ‘txdbmaker::makeTxDbPackageFromUCSC’ when loading ‘EpiTxDb’ Warning: replacing previous import ‘GenomicFeatures::makePackageName’ by ‘txdbmaker::makePackageName’ when loading ‘EpiTxDb’ Warning: replacing previous import ‘GenomicFeatures::makeFeatureDbFromUCSC’ by ‘txdbmaker::makeFeatureDbFromUCSC’ when loading ‘EpiTxDb’ ** testing if installed package keeps a record of temporary installation path * DONE (EpiTxDb)
EpiTxDb.Rcheck/tests/testthat.Rout
R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20
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> library(testthat)
> library(EpiTxDb)
Loading required package: AnnotationDbi
Loading required package: stats4
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, saveRDS, setdiff, table,
tapply, union, unique, unsplit, which.max, which.min
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: IRanges
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: Modstrings
Loading required package: Biostrings
Loading required package: XVector
Loading required package: GenomeInfoDb
Attaching package: 'Biostrings'
The following object is masked from 'package:base':
strsplit
There were 19 warnings (use warnings() to see them)
> library(RSQLite)
>
> test_check("EpiTxDb")
[ FAIL 0 | WARN 0 | SKIP 1 | PASS 257 ]
══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• On CRAN (1): 'test-4makeEpiTxDbFromtRNAdb.R:7:5'
[ FAIL 0 | WARN 0 | SKIP 1 | PASS 257 ]
>
> proc.time()
user system elapsed
7.448 0.231 7.682
EpiTxDb.Rcheck/EpiTxDb-Ex.timings
| name | user | system | elapsed | |
| EpiTxDb-class | 0.032 | 0.002 | 0.035 | |
| makeEpiTxDb | 0.051 | 0.001 | 0.052 | |
| makeEpiTxDbFromGRanges | 0.065 | 0.002 | 0.066 | |
| makeEpiTxDbFromtRNAdb | 0 | 0 | 0 | |
| modifications | 0.020 | 0.001 | 0.021 | |
| positionSequence | 0.263 | 0.003 | 0.267 | |
| rescale | 0.019 | 0.000 | 0.020 | |
| select | 0.017 | 0.000 | 0.018 | |
| shiftGenomicToTranscript | 0.799 | 0.009 | 0.808 | |