Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2024-12-24 11:47 -0500 (Tue, 24 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4754 |
palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4472 |
lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4426 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4381 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4373 |
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 1837/2274 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
scanMiRApp 1.13.0 (landing page) Pierre-Luc Germain
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
To the developers/maintainers of the scanMiRApp package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/scanMiRApp.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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
Package: scanMiRApp |
Version: 1.13.0 |
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:scanMiRApp.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings scanMiRApp_1.13.0.tar.gz |
StartedAt: 2024-12-24 10:48:52 -0000 (Tue, 24 Dec 2024) |
EndedAt: 2024-12-24 10:55:38 -0000 (Tue, 24 Dec 2024) |
EllapsedTime: 406.3 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: scanMiRApp.Rcheck |
Warnings: 5 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:scanMiRApp.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings scanMiRApp_1.13.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/scanMiRApp.Rcheck’ * using R Under development (unstable) (2024-11-24 r87369) * using platform: aarch64-unknown-linux-gnu * R was compiled by aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0 GNU Fortran (GCC) 14.2.0 * running under: openEuler 24.03 (LTS) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘scanMiRApp/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘scanMiRApp’ version ‘1.13.0’ * checking package namespace information ... OK * checking package dependencies ... INFO Imports includes 28 non-default packages. Importing from so many packages makes the package vulnerable to any of them becoming unavailable. Move as many as possible to Suggests and use conditionally. * 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 ‘scanMiRApp’ can be installed ... WARNING Found the following significant warnings: Warning: program compiled against libxml 212 using older 211 See ‘/home/biocbuild/bbs-3.21-bioc/meat/scanMiRApp.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 ... NOTE Warning: program compiled against libxml 212 using older 211 A namespace must be able to be loaded with just the base namespace loaded: otherwise if the namespace gets loaded by a saved object, the session will be unable to start. Probably some imports need to be declared in the NAMESPACE file. * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK * checking dependencies in R code ... NOTE Warning: program compiled against libxml 212 using older 211 ':::' calls which should be '::': 'BSgenome.Hsapiens.UCSC.hg38:::BSgenome.Hsapiens.UCSC.hg38' 'BSgenome.Mmusculus.UCSC.mm10:::BSgenome.Mmusculus.UCSC.mm10' 'BSgenome.Mmusculus.UCSC.mm39:::BSgenome.Mmusculus.UCSC.mm39' 'BSgenome.Rnorvegicus.UCSC.rn6:::BSgenome.Rnorvegicus.UCSC.rn6' See the note in ?`:::` about the use of this operator. * checking S3 generic/method consistency ... WARNING Warning: program compiled against libxml 212 using older 211 See section ‘Generic functions and methods’ in the ‘Writing R Extensions’ manual. * checking replacement functions ... WARNING Warning: program compiled against libxml 212 using older 211 The argument of a replacement function which corresponds to the right hand side must be named ‘value’. * checking foreign function calls ... NOTE Warning: program compiled against libxml 212 using older 211 See chapter ‘System and foreign language interfaces’ in the ‘Writing R Extensions’ manual. * checking R code for possible problems ... NOTE Warning: program compiled against libxml 212 using older 211 .fakeAnno: no visible binding for global variable 'SampleTranscript' .fakeAnno: no visible binding for global variable 'SampleKdModel' plotSitesOnUTR: no visible binding for global variable 'logKd' plotSitesOnUTR: no visible binding for global variable 'note' plotSitesOnUTR: no visible binding for global variable 'type' Undefined global functions or variables: SampleKdModel SampleTranscript logKd note type * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... NOTE Found the following Rd file(s) with Rd \link{} targets missing package anchors: enrichedMirTxPairs.Rd: findSeedMatches getTranscriptSequence.Rd: AnnotationHub, DNAStringSet Please provide package anchors for all Rd \link{} targets not in the package itself and the base packages. * checking for missing documentation entries ... WARNING Warning: program compiled against libxml 212 using older 211 All user-level objects in a package should have documentation entries. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * checking for code/documentation mismatches ... WARNING Warning: program compiled against libxml 212 using older 211 Warning: program compiled against libxml 212 using older 211 Warning: program compiled against libxml 212 using older 211 * checking Rd \usage sections ... NOTE Warning: program compiled against libxml 212 using older 211 The \usage entries for S3 methods should use the \method markup and not their full name. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * checking Rd contents ... OK * checking for unstated dependencies in examples ... 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: 5 WARNINGs, 6 NOTEs See ‘/home/biocbuild/bbs-3.21-bioc/meat/scanMiRApp.Rcheck/00check.log’ for details.
scanMiRApp.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL scanMiRApp ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library’ * installing *source* package ‘scanMiRApp’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading Warning: program compiled against libxml 212 using older 211 ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location Warning: program compiled against libxml 212 using older 211 ** testing if installed package can be loaded from final location Warning: program compiled against libxml 212 using older 211 ** testing if installed package keeps a record of temporary installation path * DONE (scanMiRApp)
scanMiRApp.Rcheck/tests/testthat.Rout
R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-unknown-linux-gnu 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(scanMiRApp) Loading required package: scanMiR Warning: program compiled against libxml 212 using older 211 > > test_check("scanMiRApp") Loading annotation Extracting transcripts Scanning with 1 thread(s) Loading annotation Extracting transcripts Scanning with 1 thread(s) Prepare miRNA model Get Transcript Sequence Scan Prepare miRNA model Get Transcript Sequence Scan [ FAIL 0 | WARN 3 | SKIP 2 | PASS 13 ] ══ Skipped tests (2) ═══════════════════════════════════════════════════════════ • On CRAN (1): 'test-shiny.R:10:3' • empty test (1): 'test-utils.R:46:1' [ FAIL 0 | WARN 3 | SKIP 2 | PASS 13 ] > > proc.time() user system elapsed 25.833 1.136 27.024
scanMiRApp.Rcheck/scanMiRApp-Ex.timings
name | user | system | elapsed | |
IndexedFst-class | 0.052 | 0.000 | 0.052 | |
ScanMiRAnno | 1.108 | 0.088 | 1.199 | |
enrichedMirTxPairs | 0.920 | 0.016 | 0.938 | |
getTranscriptSequence | 3.074 | 0.132 | 3.212 | |
plotSitesOnUTR | 2.625 | 0.088 | 2.719 | |
runFullScan | 1.375 | 0.008 | 1.386 | |
save-load-IndexedFst | 0.012 | 0.000 | 0.012 | |
scanMiRApp | 0.001 | 0.000 | 0.000 | |
scanMiRserver | 0.725 | 0.004 | 0.735 | |
scanMiRui | 0.274 | 0.004 | 0.285 | |